Give us a number, then. If 43% correspondence in an equivalent section isn't enough, what is? 50%? 75%? 99%?
It is there in the expect value.
Score E
Sequences producing significant alignments: (bits) Value
motA 567 e-162
BS_motA 91 1e-18
TM0676 74 1e-13
HP0815 68 6e-12
TP0725 68 6e-12
jhp0751 68 6e-12
BB0281 62 3e-10
aq_1003 58 6e-09
BS_ytxD 43 2e-04
PH0632 31 1.1
CT365 31 1.1
MTH1022 30 1.4
srlE 30 1.4
MTH924 30 1.8
slr0301 30 1.8
HI1728 29 3.1
Rv3689 29 4.0
jhp0817 29 4.0
acrB 29 4.0
BS_ylmB 28 5.2
acrF 28 5.2
TM1385 28 6.8
YEL031w 28 6.8
ydiS 28 6.8
acrD 28 6.8
yhiV 28 6.8
AF0134 28 6.8
Rv3091 28 8.9
BS_braB 28 8.9
sll0537 28 8.9
Notice the significant change? (Although apparently those in the know accept 10 as the cutoff for acceptance of "similarity") My phrase got 2.5. The sequence of the MOTA from the D. Vulgaris and MTH1022 when reduced to the range of 55 was IIRC ~e-05.
Score E
Sequences producing significant alignments: (bits) Value
MTH1022 506 e-144
sll0477 71 7e-13
RP309 62 5e-10
sll1404 61 9e-10
slr0677 60 2e-09
aq_1988 58 6e-09
HP1339 48 6e-06
jhp1258 48 6e-06
tolQ 47 1e-05
CT596 46 2e-05
CPn0785 46 3e-05
HI0253 45 4e-05
exbB 45 4e-05
aq_1757 45 5e-05
HI0385 45 7e-05
TM0676 44 1e-04
aq_1003 43 2e-04
MTH671 42 4e-04
HP1445 42 6e-04
jhp1338 42 6e-04
BB0281 42 6e-04
HP1130 40 0.002
jhp1058 40 0.002
HP0815 37 0.018
jhp0751 37 0.018
BS_ytxD 33 0.20
TP0725 33 0.26
PH0361 30 1.7
CT874 30 1.7
motA 30 1.7
Rv0545c 29 2.8
slr0531 29 3.7
sll0223 29 3.7
BS_motA 28 4.9
YNL189w 28 4.9
sfcA 28 4.9
ftsW 28 4.9
jhp0723 28 6.3
HP0786 28 8.3
PH0504 28 8.3
AF1017 28 8.3
Comparing only the 55--(Don't blame me this is what the Cognitor returns)
# >aq_1003
# Length = 254
#
# Score = 39.3 bits (90), Expect = 5e-04
# Identities = 21/46 (45%), Positives = 29/46 (62%), Gaps = 3/46 (6%)
#
# Query: 2 PMLGLIGTVIGIWYTFRALGVNADPAAMAEGIYVALITTILGLAVA 47
# P G+IGT+IG+ R L DP+A+ G+ VALITT+ G +A
# Sbjct: 155 PAFGMIGTLIGLIQMLRNLN---DPSALGPGMAVALITTLYGAILA 197