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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.

OK, I've figured out the problem. You're comparing apples and oranges.

Remember I also stated this ---

I also ran the X-linked ribosomal protein. In that analysis the chicken is closer to human than the primates. Go figure.

Query = gi|12653405|gb|AAH00472.1|AAH00472 ribosomal protein S4, X-linked [Homo sapiens] (263 letters)