[AndrewC]

Well, I warned you about canned programs.

Well, here is what 2 way blast shows about your comparisons. Note: the chicken protein is the same length as the human protein.

Sequence 1	gi 16307477	ribosomal protein S4, Y-linked [Homo sapiens]	Length	263	(1 .. 263)
Sequence 2	gi 1350995	40S ribosomal protein S4. This is the chicken -- Andy	Length	263	(1 .. 263)

NOTE:The statistics (bitscore and expect value) is calculated based on the size of nr database

Score =  511 bits (1317), Expect = e-144
Identities = 247/263 (93%), Positives = 254/263 (95%)

Query:          1   MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDE 60
                    MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLI+FLRNRLKYALTGDE
Sbjct:          1   MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE 60
S4 RNA-BINDING. 42                                           *******************
RPS4            1   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          61  VKKICMQRFIKIDGKVRVDVTYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAK 120
                    VKKICMQRFIKIDGKVR D+TYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRIT EEAK
Sbjct:          61  VKKICMQRFIKIDGKVRTDITYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITAEEAK 120
S4 RNA-BINDING. 61  ********************************************
RPS4            61  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          121 YKLCKVRKITVGVKGIPHLVTHDARTIRYPDPVIKVNDTVQIDLGTGKIINFIKFDTGNL 180
                    YKLCKVRKI VG KGIPHLVTHDARTIRYPDP+IKVNDT+QIDL TGKI +FIKFDTGNL
Sbjct:          121 YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL 180
RPS4            121 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          181 CMVIGGANLGRVGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPR 240
                    CMV GGANLGR+GVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIG GNKPWISLPR
Sbjct:          181 CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR 240
RPS4            181 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          241 GKGIRLTVAEERDKRLATKQSSG 263
                    GKGIRLT+AEERDKRLA KQSSG
Sbjct:          241 GKGIRLTIAEERDKRLAAKQSSG 263
RPS4            241 +++++++++++++++++++++++

Sequence 1	gi 16307477	ribosomal protein S4, Y-linked [Homo sapiens]	Length	263	(1 .. 263)
Sequence 2	gi 4432942	ribosomal protein S4 [Sus scrofa]	Length	194	(1 .. 194)

NOTE:The statistics (bitscore and expect value) is calculated based on the size of nr database

Score =  371 bits (953), Expect = e-102
Identities = 178/194 (91%), Positives = 187/194 (95%)

Query: 20  LDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVD 79
           LDKLTGVFAPRPSTGPHKLRECLPLI+FLRNRLKYALTGDEVKKICMQRFIKIDGKVR D
Sbjct: 1   LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD 60

Query: 80  VTYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHL 139
           +TYPAGFMDVISI+KTGE+FRL+YDTKGRFAVHRIT EEAKYKLCKVRKI VG KGIPHL
Sbjct: 61  ITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL 120

Query: 140 VTHDARTIRYPDPVIKVNDTVQIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRE 199
           VTHDARTIRYPDP+IKVNDT+QIDL TGKI +FIKFDTGNLCMV GGANLGR+GVITNRE
Sbjct: 121 VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE 180

Query: 200 RHPGSFDVVHVKDA 213
           RHPGSFDVVHVKDA
Sbjct: 181 RHPGSFDVVHVKDA 194

Sequence 1	gi 4432939	ribosomal protein S4 [Bos taurus]	Length	194	(1 .. 194)
Sequence 2	gi 4432942	ribosomal protein S4 [Sus scrofa]	Length	194	(1 .. 194)

NOTE:The statistics (bitscore and expect value) is calculated based on the size of nr database

Score =  395 bits (1014), Expect = e-109
Identities = 192/194 (98%), Positives = 193/194 (98%)

Query: 1   LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD 60
           LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD
Sbjct: 1   LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD 60

Query: 61  VTYPAGFMDVISIDKIGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL 120
           +TYPAGFMDVISIDK GENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
Sbjct: 61  ITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL 120

Query: 121 VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE 180
           VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE
Sbjct: 121 VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE 180

Query: 181 RHPGSFDVVHVKDA 194
           RHPGSFDVVHVKDA
Sbjct: 181 RHPGSFDVVHVKDA 194

---

Here I grabbed the pieces from the chicken and the human protein in order to compare the same range as the pig. I think that this is not the correct way to analyze the data but as you can see the chicken still wins by 181 to 178.

Sequence 1	lcl|seq_1 This is chicken -- Andy		Length	194	(1 .. 194)
Sequence 2	lcl|seq_2 This is human -- Andy		Length	194	(1 .. 194)

NOTE:The statistics (bitscore and expect value) is calculated based on the size of nr database

Score =  376 bits (966), Expect = e-103
Identities = 181/194 (93%), Positives = 187/194 (96%)

Query: 1   LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD 60
           LDKLTGVFAPRPSTGPHKLRECLPLI+FLRNRLKYALTGDEVKKICMQRFIKIDGKVR D
Sbjct: 1   LDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVD 60

Query: 61  ITYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITAEEAKYKLCKVRKIFVGTKGIPHL 120
           +TYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRIT EEAKYKLCKVRKI VG KGIPHL
Sbjct: 61  VTYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHL 120

Query: 121 VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE 180
           VTHDARTIRYPDP+IKVNDT+QIDL TGKI +FIKFDTGNLCMV GGANLGR+GVITNRE
Sbjct: 121 VTHDARTIRYPDPVIKVNDTVQIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRE 180

Query: 181 RHPGSFDVVHVKDA 194
           RHPGSFDVVHVKDA
Sbjct: 181 RHPGSFDVVHVKDA 194

[Right Wing Professor]

OK, I've figured out the problem. You're comparing apples and oranges. Humans have two rps4 proteins; one Y linked, one X-linked. The pig only has one, as has the chicken. The human X linked is the protein that's homologous to the pig and chicken genes. (Which makes sense; girls have ribosomes as well; I wonder is the y-linked gene ever expressed?)

Sequence 1 gi 4432942 ribosomal protein S4 [Sus scrofa] Length 194 (1 .. 194)

Sequence 2 gi 1350997 40S ribosomal protein S4, X isoform (Single copy abundant mRNA protein) (SCR10). Length 263 (1 .. 263)

Score =  397 bits (1021), Expect = e-110 
Identities = 194/194 (100%), Positives = 194/194 (100%) 

Query:          1   LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD 60
                    LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD
Sbjct:          20  LDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTD 79
Conflict        57                                       ***
S4 RNA-BINDING. 42                        **************************************
Conflict        33               *
RPS4X           20  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          61  ITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL 120
                    ITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
Sbjct:          80  ITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL 139
S4 RNA-BINDING. 80  *************************
RPS4X           80  ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          121 VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE 180
                    VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE
Sbjct:          140 VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRE 199
RPS4X           140 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Query:          181 RHPGSFDVVHVKDA 194
                    RHPGSFDVVHVKDA
Sbjct:          200 RHPGSFDVVHVKDA 213
RPS4X           200 ++++++++++++++

In yet another respect, humans really are identical to pigs.

In contrast, humans/pigs have 4 mismatches with the same chicken sequence.