RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1302
(225 letters)
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 37.0 bits (86), Expect = 0.006
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 7 ELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
EL + EE EE+R S LE+E++ K+L + ++ ++Q Q + + R LE+
Sbjct: 261 ELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEE 320
Query: 67 SQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
+ +L + KL EEL LE++L
Sbjct: 321 LEAQLEEL--ESKLDELA----EELAELEEKL 346
Score = 35.4 bits (82), Expect = 0.020
Identities = 21/116 (18%), Positives = 49/116 (42%), Gaps = 16/116 (13%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ ++ EL++ E E+ S L +E++ +KL ++ + E ++ I ++ + + +
Sbjct: 889 LALLRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEE 948
Query: 61 RRDLEQSQDELLKDL------------KLRKLIIE----NFIPIEELKRLEQRLVY 100
+ + L + +L I E N IEE + L++R +
Sbjct: 949 YSLTLEEAEALENKIEDDEEEARRRLKRLENKIKELGPVNLAAIEEYEELKERYDF 1004
Score = 31.6 bits (72), Expect = 0.42
Identities = 23/98 (23%), Positives = 52/98 (53%), Gaps = 6/98 (6%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ + E+++ EE EE+ L E + + L + S+ EE+ ++++++ + +
Sbjct: 854 IESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSEL 913
Query: 61 RRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
RR+LE+ +++ L L+LR +E + L++RL
Sbjct: 914 RRELEELREK-LAQLELRLEGLEV-----RIDNLQERL 945
Score = 31.2 bits (71), Expect = 0.48
Identities = 15/70 (21%), Positives = 45/70 (64%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
++E ++E+++ EE EE+ + LE+ + K+L+++ + E+++++++++ + +
Sbjct: 672 ILERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISAL 731
Query: 61 RRDLEQSQDE 70
R+DL + + E
Sbjct: 732 RKDLARLEAE 741
Score = 30.4 bits (69), Expect = 0.80
Identities = 18/69 (26%), Positives = 35/69 (50%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+K+EL+ E EE+ LE ++ ++L+ + SK +++ I + +E R
Sbjct: 348 ELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEA 407
Query: 63 DLEQSQDEL 71
LE+ +D
Sbjct: 408 RLERLEDRR 416
Score = 28.5 bits (64), Expect = 3.4
Identities = 23/99 (23%), Positives = 50/99 (50%), Gaps = 7/99 (7%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E++ L++ EE E +R + LE ++ + N +++++ E + ++D + ++
Sbjct: 369 ELESRLEELEEQLETLRSKVAQLELQIASLNNEIERL----EARLERLEDRRERLQQEIE 424
Query: 63 DLEQSQDELLKDL---KLRKLIIENFIPIEELKRLEQRL 98
+L + +E +L +L E EEL+RLE+ L
Sbjct: 425 ELLKKLEEAELKELQAELEELEEELEELQEELERLEEAL 463
Score = 27.7 bits (62), Expect = 6.3
Identities = 12/69 (17%), Positives = 39/69 (56%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+++E+++ ++ + S LEQ+ Q ++L + + EE++ ++++ + +
Sbjct: 278 ELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAE 337
Query: 63 DLEQSQDEL 71
+L + +++L
Sbjct: 338 ELAELEEKL 346
Score = 27.3 bits (61), Expect = 8.6
Identities = 22/100 (22%), Positives = 45/100 (45%), Gaps = 2/100 (2%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDL 64
+EL ++ + EE + QE++ K ++L+ S+ EE +++Q + + L
Sbjct: 241 LEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRL 300
Query: 65 EQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEES 104
E Q + + +L L + +L+ LE +L E
Sbjct: 301 E--QQKQILRERLANLERQLEELEAQLEELESKLDELAEE 338
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 35.6 bits (83), Expect = 0.019
Identities = 28/102 (27%), Positives = 50/102 (49%), Gaps = 12/102 (11%)
Query: 2 IEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQ----KIYSKYE-EVKQDIQDIMDE 56
E+++EL++K E E + L++E++ K +KLQ K+ + E E +Q I++ E
Sbjct: 526 EELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKE 585
Query: 57 FNRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
+ ++L Q Q +K +L IE KRL +
Sbjct: 586 ADEIIKELRQLQKGGYASVKAHEL-------IEARKRLNKAN 620
Score = 32.5 bits (75), Expect = 0.16
Identities = 10/66 (15%), Positives = 37/66 (56%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDL 64
K+ + + +E E+ + LE+E++ K ++ + + + E++K+++++ ++ + L
Sbjct: 508 KKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKL 567
Query: 65 EQSQDE 70
+ ++
Sbjct: 568 LEEAEK 573
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 33.8 bits (78), Expect = 0.043
Identities = 18/102 (17%), Positives = 47/102 (46%), Gaps = 20/102 (19%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQE----------VQAKNKKLQKIYSKYEEVKQDI 50
+ E++QEL + +E E++ + L+QE ++A+ ++LQK ++ +++ +
Sbjct: 68 LPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANA 127
Query: 51 QDIMDEFNR----------DRRDLEQSQDELLKDLKLRKLII 82
++ +E + LE + L ++ + R +
Sbjct: 128 IELDEENRELREELAELKQENEALEAENERLQENEQRRWFLY 169
Score = 30.0 bits (68), Expect = 0.82
Identities = 16/60 (26%), Positives = 33/60 (55%)
Query: 24 TLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIE 83
L+QE+ ++L ++ + E++Q+ Q++ E + +LE+ Q EL + +L IE
Sbjct: 70 ELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIE 129
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 33.5 bits (77), Expect = 0.088
Identities = 26/96 (27%), Positives = 54/96 (56%), Gaps = 6/96 (6%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+++E+++ EE +E+ LE+E++ ++L+++ E K++++D + E ++
Sbjct: 832 ELEEEIEELEEKLDELEEELEELEKELEELKEELEEL----EAEKEELEDELKELEEEKE 887
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
+LE+ EL +L K IE E L+ LE +L
Sbjct: 888 ELEEELRELESELAELKEEIEKL--RERLEELEAKL 921
Score = 33.1 bits (76), Expect = 0.13
Identities = 25/99 (25%), Positives = 55/99 (55%), Gaps = 3/99 (3%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+K+EL++ E EE+ LE+E + ++L+++ S+ E+K++I+ + +
Sbjct: 860 ELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEA 919
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIE---ELKRLEQRL 98
LE+ + EL + + + E+ + E E++RLE+ +
Sbjct: 920 KLERLEVELPELEEELEEEYEDTLETELEREIERLEEEI 958
Score = 32.0 bits (73), Expect = 0.23
Identities = 24/97 (24%), Positives = 54/97 (55%), Gaps = 1/97 (1%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+++EL++ EE EE++ LE+E+++ + L K+ + EE+++ Q + +E
Sbjct: 741 ELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEE 800
Query: 63 DLEQSQDELLK-DLKLRKLIIENFIPIEELKRLEQRL 98
+LE+++ L + +L L +E++ LE+ +
Sbjct: 801 ELEEAERRLDALERELESLEQRRERLEQEIEELEEEI 837
Score = 32.0 bits (73), Expect = 0.31
Identities = 22/97 (22%), Positives = 53/97 (54%), Gaps = 6/97 (6%)
Query: 7 ELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
+L + + EE+ S LE+E++ ++L++ + EE+K +++++ +E + +L +
Sbjct: 233 KLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLE 292
Query: 67 SQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEE 103
++E +++L+ ++ E L+ LE L EE
Sbjct: 293 LKEE-IEELEGEISLLR-----ERLEELENELEELEE 323
Score = 31.6 bits (72), Expect = 0.33
Identities = 23/106 (21%), Positives = 57/106 (53%), Gaps = 8/106 (7%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDE---F 57
+ E++ +L+K EE + ++ +LE ++ ++L+++ + EE+K+++ + +E
Sbjct: 676 LAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQL 735
Query: 58 NRDRRDLEQSQDELLKDL-----KLRKLIIENFIPIEELKRLEQRL 98
+LE+ +EL ++L +L +L E E L +L++ +
Sbjct: 736 QSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEI 781
Score = 30.5 bits (69), Expect = 0.92
Identities = 19/97 (19%), Positives = 51/97 (52%), Gaps = 5/97 (5%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKI---YSKYEEVKQDIQDIMDEFNRDR 61
++EL + EE EE++ E+E++ +L+++ + +E ++++ ++E +
Sbjct: 245 EEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEI 304
Query: 62 RDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
L + +EL +L+ + +E E+++ L++ L
Sbjct: 305 SLLRERLEELENELEELEERLEEL--KEKIEALKEEL 339
Score = 30.1 bits (68), Expect = 1.1
Identities = 22/110 (20%), Positives = 57/110 (51%), Gaps = 16/110 (14%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKN--KKLQK---------IYSKYEEVKQDIQ 51
++ L++ E+ EE+ LE++ + ++L+ + +K +E++++++
Sbjct: 183 RTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELE 242
Query: 52 DIMDEFNRDRRDLE---QSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
++ +E +R +LE + +E K+++ K +E EEL+ L++ L
Sbjct: 243 ELEEELSRLEEELEELQEELEEAEKEIEELKSELEEL--REELEELQEEL 290
Score = 29.7 bits (67), Expect = 1.6
Identities = 16/82 (19%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
+ + L+ +E +E+ L+ E++ N++L+++ + EE++ ++++ E +
Sbjct: 415 RLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQE 474
Query: 63 DLEQSQDELLKDLKLRKLIIEN 84
+L++ + E L L+ R +E
Sbjct: 475 ELQRLEKE-LSSLEARLDRLEA 495
Score = 29.7 bits (67), Expect = 1.6
Identities = 24/104 (23%), Positives = 49/104 (47%), Gaps = 8/104 (7%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQA---KNKKLQKIYSKYEEVKQDIQDIMDEFNR 59
++ L++ EE+ L++E+ A + ++LQ + EE +++++ ++E
Sbjct: 699 SLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQE 758
Query: 60 DRRDLEQSQDELLKDLKLRKLIIENFIPI-----EELKRLEQRL 98
+LE+ + L + L K IE EEL+ LE+ L
Sbjct: 759 RLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEEL 802
Score = 28.1 bits (63), Expect = 4.1
Identities = 23/97 (23%), Positives = 53/97 (54%), Gaps = 5/97 (5%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E++++ +E EE+ E+ + A ++L+ + + E ++Q+I+++ +
Sbjct: 783 ELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEEL----EEEIE 838
Query: 63 DLEQSQDELLKDLK-LRKLIIENFIPIEELKRLEQRL 98
+LE+ DEL ++L+ L K + E +EEL+ ++ L
Sbjct: 839 ELEEKLDELEEELEELEKELEELKEELEELEAEKEEL 875
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 33.1 bits (76), Expect = 0.095
Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 10/84 (11%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDL 64
+QEL E R L+QE+Q + E + ++++E +
Sbjct: 213 RQELRSLSVKISEKRKQLEELQQELQELTIAI-------EALTNKKSELLEEIAEAEKIR 265
Query: 65 EQSQD---ELLKDLKLRKLIIENF 85
E+ + + + LK + +++
Sbjct: 266 EECRGWSAKEISKLKAKVSLLQKL 289
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 32.8 bits (76), Expect = 0.12
Identities = 10/46 (21%), Positives = 25/46 (54%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDI 50
+ L+K+EE E+ +QE++ K ++L+++ + + + I
Sbjct: 102 LELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELERI 147
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 32.8 bits (75), Expect = 0.13
Identities = 21/104 (20%), Positives = 52/104 (50%), Gaps = 3/104 (2%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMD---EF 57
I + + + EE EE LE+E++ ++L+++ K E++Q I+++ E
Sbjct: 669 EIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAEL 728
Query: 58 NRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYD 101
+++LE+ + L +LR+ + + + + L+ L ++ +
Sbjct: 729 EELKKELEKLEKALELLEELREKLGKAGLRADILRNLLAQIEAE 772
Score = 28.6 bits (64), Expect = 3.2
Identities = 18/90 (20%), Positives = 48/90 (53%), Gaps = 2/90 (2%)
Query: 9 DKKEESTEEIRGNYSTLEQEVQAKNKK--LQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
+K EE EIR +E E Q + K L+++ + E++++++++++ + + +E+
Sbjct: 661 EKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEE 720
Query: 67 SQDELLKDLKLRKLIIENFIPIEELKRLEQ 96
+ + +L+K + + +E L+ L +
Sbjct: 721 LESRKAELEELKKELEKLEKALELLEELRE 750
Score = 28.6 bits (64), Expect = 3.2
Identities = 20/101 (19%), Positives = 50/101 (49%), Gaps = 5/101 (4%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD-- 60
E+++E+++ E+ E+ L + +A ++L++ K E + ++++++ ++
Sbjct: 498 ELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQL 557
Query: 61 ---RRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
R LE EL + L+ +L+ +EEL+ + L
Sbjct: 558 KEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKEL 598
Score = 28.6 bits (64), Expect = 3.6
Identities = 19/98 (19%), Positives = 44/98 (44%), Gaps = 5/98 (5%)
Query: 7 ELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
EL+++ +E L +E++ K+L+++ + E+ + + + +E LE
Sbjct: 485 ELEEELSREKEEA----ELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLEN 540
Query: 67 SQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEES 104
E L++LK + + + + +L+ Q L E
Sbjct: 541 -LLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEE 577
Score = 27.0 bits (60), Expect = 10.0
Identities = 17/88 (19%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 11 KEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDE 70
+ + EE+ LE E++ + ++++ + EE ++++ + +E + R +LE+ +
Sbjct: 652 LQAALEELEEKVEELEAEIRRELQRIENEE-QLEEKLEELEQLEEELEQLREELEELLKK 710
Query: 71 LLKDLKLRKLIIENFIPIEELKRLEQRL 98
L + +L + + EL+ L++ L
Sbjct: 711 LGEIEQLIEELESR---KAELEELKKEL 735
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 32.4 bits (74), Expect = 0.18
Identities = 26/185 (14%), Positives = 63/185 (34%), Gaps = 18/185 (9%)
Query: 35 KLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRL 94
L++ E +++++ ++ ++ +LE+ + L ++ + + EN + EL L
Sbjct: 71 DLEEEILDLEAEIKEVEENLESLEKEINELEEWLNVLDEE---KSFLDENLEELSELSNL 127
Query: 95 EQRLVYDEESSQWNIVPETNPFYIQKRLVASPQLRRPTTLKARE-----KISQCPTDAGK 149
+ Y + + I + + R R +I + D K
Sbjct: 128 DIDFKYLRGAEGLKLGFVAG--VINREKL--EAFERELWRACRGYIRQAEIEEPLEDPKK 183
Query: 150 TRFI----GENILTLNFDICPN-NCKNYQGPKVAPSILSVLQAALQDEADIDVDVKSTAS 204
T FI G+ L I + + Y P+ ++ + ++ V
Sbjct: 184 TVFIIFFVGKEDLDKVKKILDSFGFELYDVPETEGERSELISKVNKRIEELQ-RVLEQTE 242
Query: 205 KKIHR 209
+ +
Sbjct: 243 SHLEK 247
Score = 30.4 bits (69), Expect = 0.72
Identities = 21/109 (19%), Positives = 50/109 (45%), Gaps = 15/109 (13%)
Query: 5 KQELDKKEESTEEIRGN-YSTLEQE------VQAKNKKLQKIYSKYEEVKQDIQDIMDE- 56
K++LDK ++ + Y E E + NK+++++ E+ + ++ ++ +
Sbjct: 193 KEDLDKVKKILDSFGFELYDVPETEGERSELISKVNKRIEELQRVLEQTESHLEKVLVKI 252
Query: 57 ----FNRDRR-DLEQSQDELLKDLKL--RKLIIENFIPIEELKRLEQRL 98
D + E++ E L + LI E ++P ++L++L+ L
Sbjct: 253 ADELLAWDEQVSKEKAVYETLNLFNYDTKTLIAEGWVPAKDLEKLKAAL 301
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 32.3 bits (73), Expect = 0.21
Identities = 24/98 (24%), Positives = 48/98 (48%), Gaps = 4/98 (4%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
+ EL KKE+ +E+ G + + K K++ ++ +K ++V +DIQ + ++
Sbjct: 713 STESELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPELRNKLQKVNRDIQRLKNDIEEQET 772
Query: 63 DLE--QSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
L ++E K I+E F ELK +E+++
Sbjct: 773 LLGTIMPEEESAKVCLTDVTIMERF--QMELKDVERKI 808
>gnl|CDD|218762 pfam05816, TelA, Toxic anion resistance protein (TelA). This
family consists of several prokaryotic TelA like
proteins. TelA and KlA are associated with tellurite
resistance and plasmid fertility inhibition.
Length = 333
Score = 31.4 bits (72), Expect = 0.28
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 33 NKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLK-LRKLIIENFIPIEEL 91
+++ ++KY+ V I I+ E LE+ +DELLKD L +L +N E
Sbjct: 83 KNSIERYFAKYQSVGGQIDKILVE-------LEKGKDELLKDNAMLDQLYDKNL---EYY 132
Query: 92 KRLEQ 96
+ LE+
Sbjct: 133 EELEK 137
>gnl|CDD|235515 PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated.
Length = 220
Score = 31.3 bits (72), Expect = 0.29
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 173 QGPKVAPSILSVLQAALQDEADIDVDVKSTASKKIH 208
+ +APSILS A L +E V++ + IH
Sbjct: 2 KMVLIAPSILSADFARLGEEVK---AVEAAGADWIH 34
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 31.7 bits (72), Expect = 0.29
Identities = 14/59 (23%), Positives = 30/59 (50%)
Query: 27 QEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENF 85
QE+ ++ K L+ KY ++ I+DI + ++ + E++ ++K K I+ F
Sbjct: 14 QEITSEEKYLKDKLDKYNHLRNRIEDIEVLCEMMSEEDDEMKKEIISEVKNIKEEIDRF 72
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 31.4 bits (71), Expect = 0.33
Identities = 25/107 (23%), Positives = 54/107 (50%), Gaps = 8/107 (7%)
Query: 7 ELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
E +E EE++ L++E + K+L+++ ++YEEV++ ++ + E +R LE+
Sbjct: 129 EYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSR----LEE 184
Query: 67 SQDELLKDL-KLRKLIIENFIPIEELKRLEQRLVYDEESSQWNIVPE 112
+L ++ L+K E ++ E+ L+ D N+ P+
Sbjct: 185 MLKKLPGEVYDLKKRWDELE---PGVELPEEELISDLVKETLNLAPK 228
Score = 29.5 bits (66), Expect = 1.3
Identities = 20/111 (18%), Positives = 55/111 (49%), Gaps = 5/111 (4%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+K++L++ ++ EE+ LE E + ++L+++ + +++ ++ + E ++
Sbjct: 139 ELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKK 198
Query: 63 DLEQSQD--ELLKDLKLRKLIIENFIPIEELKRLE-QRLVYDEESSQWNIV 110
++ + EL ++ + L+ E K +E Q +Y E+ + I+
Sbjct: 199 RWDELEPGVELPEEELISDLVKETL--NLAPKDIEGQGYIYAEDEKEVEIL 247
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 31.5 bits (72), Expect = 0.34
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 27 QEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLII 82
+ +A+ L K+ +V Q+IQ+ D R + S EL + +R+ ++
Sbjct: 202 KLEEAR-AVLAKL-RGVSDVDQEIQEEKDSLERSVEAEKASWLELFRGKTVRQRLL 255
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 31.6 bits (72), Expect = 0.37
Identities = 22/103 (21%), Positives = 49/103 (47%), Gaps = 7/103 (6%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQ---DIMDEFNR 59
E+++EL++ E + ++ L++E +L+++ K EE++ I+ + E
Sbjct: 865 ELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKA 924
Query: 60 DRRDLEQSQDELLKDLKLRKLIIENFIPIE----ELKRLEQRL 98
LE+ E+ + I E + +E EL+R+E+ +
Sbjct: 925 KLEALEEELSEIEDPKGEDEEIPEEELSLEDVQAELQRVEEEI 967
Score = 31.2 bits (71), Expect = 0.47
Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 6/96 (6%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
++ E+++ E EE R L +E ++L+ + ++ EEV ++ + DE R
Sbjct: 333 KLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYRE 392
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
LE+ + E + +L E EEL+RL + L
Sbjct: 393 KLEKLKRE------INELKRELDRLQEELQRLSEEL 422
Score = 30.4 bits (69), Expect = 0.93
Identities = 17/71 (23%), Positives = 35/71 (49%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+ QEL EI LEQE + ++L+++ ++Q+I+++ E
Sbjct: 706 ELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEA 765
Query: 63 DLEQSQDELLK 73
+E+ +++L K
Sbjct: 766 RIEELEEDLHK 776
Score = 29.3 bits (66), Expect = 1.7
Identities = 10/81 (12%), Positives = 43/81 (53%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ +K+++ + E + + + E+E++ ++L K+ ++ +++ +I+++ E +
Sbjct: 289 QLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEE 348
Query: 61 RRDLEQSQDELLKDLKLRKLI 81
R+ ++ +E + + + +
Sbjct: 349 RKRRDKLTEEYAELKEELEDL 369
Score = 28.9 bits (65), Expect = 2.8
Identities = 10/62 (16%), Positives = 30/62 (48%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDL 64
+ ++++ EE E+ E +++ L K + ++K++ + E ++ +R+L
Sbjct: 433 EAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQREL 492
Query: 65 EQ 66
+
Sbjct: 493 AE 494
Score = 28.5 bits (64), Expect = 3.1
Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 6/97 (6%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E++ EL K EE I +EQ++ + + + E+ Q++Q+ + +
Sbjct: 795 EIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYL----EKEIQELQEQRIDLKEQIK 850
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLV 99
+E+ + L + + +E L+ LE RL
Sbjct: 851 SIEKEIENLNGKKEELEEELEEL--EAALRDLESRLG 885
Score = 28.1 bits (63), Expect = 4.2
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 6/101 (5%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
+++ L+ + ++ +E + +++L K E++++I+ + E + +
Sbjct: 678 RLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKE 737
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEE 103
LE+ ++ L L E ELK LE R+ EE
Sbjct: 738 RLEELEE------DLSSLEQEIENVKSELKELEARIEELEE 772
Score = 28.1 bits (63), Expect = 4.5
Identities = 26/108 (24%), Positives = 51/108 (47%), Gaps = 5/108 (4%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDI---MDEF 57
I++K+++ E+ E + G LE+E++ L+ + S+ ++K++ ++ + E
Sbjct: 842 RIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLREL 901
Query: 58 NRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEESS 105
R +LE ++ K L K +E EEL +E DEE
Sbjct: 902 ERKIEELEAQIEKKRKRLSELKAKLEAL--EEELSEIEDPKGEDEEIP 947
Score = 28.1 bits (63), Expect = 4.5
Identities = 22/99 (22%), Positives = 48/99 (48%), Gaps = 3/99 (3%)
Query: 2 IEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDR 61
E+K+EL+ EE+ ++ E++ +KL+K+ + E+K+++ + +E R
Sbjct: 360 AELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLS 419
Query: 62 RDLEQSQDELLKDL--KLRKLIIENFIPIEELKRLEQRL 98
+L + + K+ +L E E+K+ E +L
Sbjct: 420 EELADLNAA-IAGIEAKINELEEEKEDKALEIKKQEWKL 457
Score = 27.7 bits (62), Expect = 5.5
Identities = 14/69 (20%), Positives = 31/69 (44%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
+ +EL + I + LE+E + K +++K K E++ D+ E +
Sbjct: 417 RLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKE 476
Query: 63 DLEQSQDEL 71
+ ++ + EL
Sbjct: 477 EYDRVEKEL 485
Score = 27.3 bits (61), Expect = 8.9
Identities = 24/98 (24%), Positives = 49/98 (50%), Gaps = 2/98 (2%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYS-KYEEVKQDIQDIMDEFNRDR 61
+++EL+K E E+ +EQ ++ NKK++ + + VK+ I ++ E
Sbjct: 248 SLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLE 307
Query: 62 RDLEQSQDELLK-DLKLRKLIIENFIPIEELKRLEQRL 98
R + + + EL + +L KL E + E++ LE+ +
Sbjct: 308 RSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREI 345
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 31.1 bits (71), Expect = 0.43
Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 10/100 (10%)
Query: 3 EMKQELDKKEES----TEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFN 58
E+K+EL K EE EI LE+ K K ++ ++ + + N
Sbjct: 99 ELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWK--KLAKKYDSNLSEALKGLN 156
Query: 59 RDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
+ E+ LLK+LK L + + +EELK + L
Sbjct: 157 YKKNFKEK----LLKELKSVILNASSLLSLEELKAKIKTL 192
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 30.9 bits (70), Expect = 0.56
Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
E K+E++ E + EQ+ + K L++ +E++Q+++++ +
Sbjct: 506 YGEFKEEINVLIEKLSALEKEL---EQKNEHLEKLLKEQEKLKKELEQEMEELKERERNK 562
Query: 61 RRDLEQSQDELLKDLK 76
+ +LE+ E LK LK
Sbjct: 563 KLELEKEAQEALKALK 578
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 30.7 bits (70), Expect = 0.59
Identities = 16/87 (18%), Positives = 40/87 (45%), Gaps = 16/87 (18%)
Query: 24 TLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELL----------- 72
T + ++ ++L++I + E + ++++ E + + + E L
Sbjct: 212 TPSELIREIKEELEEIEKERESLLEELK----ELAKKYLEELLALYEYLEIELERAEALS 267
Query: 73 KDLKLRKL-IIENFIPIEELKRLEQRL 98
K LK K IE ++P + +K+L++ +
Sbjct: 268 KFLKTDKTFAIEGWVPEDRVKKLKELI 294
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 30.4 bits (69), Expect = 0.63
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDI---MDEFNR 59
++ E D+ E +EIR + E++A NK L+ + + E+++ + + + E
Sbjct: 14 KLDLEKDRLEPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRE 73
Query: 60 DRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLV 99
+ E+ + + +LR L IE I E + LE L
Sbjct: 74 RIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELA 113
>gnl|CDD|118696 pfam10168, Nup88, Nuclear pore component. Nup88 can be divided
into two structural domains; the N-terminal two-thirds
of the protein has no obvious structural motifs but is
the region for binding to Nup98, one of the components
of the nuclear pore. the C-terminal end is a predicted
coiled-coil domain. Nup88 is overexpressed in tumour
cells.
Length = 717
Score = 30.6 bits (69), Expect = 0.75
Identities = 12/56 (21%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 4 MKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNR 59
+K +KE+ E+I+ +E ++ +++ +K+ K+EE K + + +++ R
Sbjct: 567 VKLLQLQKEKQLEDIQ----DCREERKSLSERAEKLAEKFEEAKYNQELLVNRCKR 618
>gnl|CDD|215689 pfam00067, p450, Cytochrome P450. Cytochrome P450s are
haem-thiolate proteins involved in the oxidative
degradation of various compounds. They are particularly
well known for their role in the degradation of
environmental toxins and mutagens. They can be divided
into 4 classes, according to the method by which
electrons from NAD(P)H are delivered to the catalytic
site. Sequence conservation is relatively low within the
family - there are only 3 absolutely conserved residues
- but their general topography and structural fold are
highly conserved. The conserved core is composed of a
coil termed the 'meander', a four-helix bundle, helices
J and K, and two sets of beta-sheets. These constitute
the haem-binding loop (with an absolutely conserved
cysteine that serves as the 5th ligand for the haem
iron), the proton-transfer groove and the absolutely
conserved EXXR motif in helix K. While prokaryotic P450s
are soluble proteins, most eukaryotic P450s are
associated with microsomal membranes. their general
enzymatic function is to catalyze regiospecific and
stereospecific oxidation of non-activated hydrocarbons
at physiological temperatures.
Length = 461
Score = 30.3 bits (69), Expect = 0.77
Identities = 10/56 (17%), Positives = 24/56 (42%)
Query: 36 LQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENFIPIEEL 91
K + ++ I+D++D+ +RR+ S + +D L+ + +L
Sbjct: 202 PGPHGRKLKRARKKIKDLLDKLIEERRETLDSAKKSPRDFLDALLLAKEEEDGSKL 257
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 29.5 bits (67), Expect = 0.79
Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 6 QELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVK-----QDIQDIMDEFNRD 60
E + + +++ + L+ E+Q K K+LQK K ++ + + E +
Sbjct: 28 SESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQK 87
Query: 61 RRDLEQSQDELLKDLKLR 78
+++L+Q Q ++L+ +
Sbjct: 88 QQELQQKQQAAQQELQQK 105
Score = 28.8 bits (65), Expect = 1.5
Identities = 19/83 (22%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKL--QKIYSKYEEVKQDIQDIMDEFNRD 60
++++E K + ++ EQ++Q + L + +K +E++Q Q++ +
Sbjct: 39 QLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQELQQKQQAA 98
Query: 61 RRDLEQSQDELLKDL--KLRKLI 81
+++L+Q Q ELL+ + K+ K I
Sbjct: 99 QQELQQKQQELLQPIYDKIDKAI 121
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 29.7 bits (67), Expect = 0.85
Identities = 15/98 (15%), Positives = 53/98 (54%), Gaps = 6/98 (6%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ ++++ + + E E+++ + L + +++ ++L+ + +E+ ++++++ +D
Sbjct: 95 LEDLEERIAELESELEDLKEDLQLLRELLKSLEERLESLEESIKELAKELREL----RQD 150
Query: 61 RRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
R+ + E L+ L+ ++ I+EL+ L ++L
Sbjct: 151 LREEVEELREELERLQENLQRLQEA--IQELQSLLEQL 186
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 30.4 bits (69), Expect = 0.86
Identities = 21/96 (21%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E ++ +++K E EE+R + LE E + K + + + EE ++++ E N
Sbjct: 527 ERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEV----AELNSKLA 582
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRL 98
+L++ + L + L I + +E++RL ++
Sbjct: 583 ELKERIESLERIRTLLAAIADA---EDEIERLREKR 615
Score = 29.6 bits (67), Expect = 1.4
Identities = 17/65 (26%), Positives = 36/65 (55%)
Query: 7 ELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
+ D EE EE+R + LE E++ + ++ + EE++++I+++ + F DL
Sbjct: 350 DADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRERFGDAPVDLGN 409
Query: 67 SQDEL 71
++D L
Sbjct: 410 AEDFL 414
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 30.2 bits (68), Expect = 0.93
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 19 RGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEF--NRDRRDLEQSQDELLKDL 75
+G+Y T E+ + + K QK + E + +Q +D+F N R L QS+ + L L
Sbjct: 423 KGDYDTFERTREEQLKNQQKAFESNERSRSHMQAFIDKFRYNAKRASLVQSRIKALDRL 481
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 29.8 bits (67), Expect = 1.0
Identities = 30/115 (26%), Positives = 54/115 (46%), Gaps = 8/115 (6%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVK---QDIQDIMDEFNRDR 61
KQ L K E EI NY L+ E+ K+ +++ + EE++ D+ + E ++
Sbjct: 49 KQYLSKLESQNVEIS-NYEALDSELDELKKEEERLLDELEELEKEDDDLDGELVELQEEK 107
Query: 62 RDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEESSQWNIVPETNPF 116
LE + + L++ L N + L+ LE L Y+ +Q + + +TN F
Sbjct: 108 EQLENEELQYLREYNLFD--RNNLQLEDNLQSLE--LQYEYSLNQLDKLRKTNIF 158
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 30.2 bits (68), Expect = 1.1
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 9/100 (9%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+ E D+ E+T + +Y + E +++ + EEV+ ++ DI +E+N +R+
Sbjct: 163 ELDAERDRLIEATRRLSVDYVPEDDEFVDDIGDDERLTA--EEVRAEVADIYEEYN-ERK 219
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDE 102
L + + ++ ++L I E L R E RL Y
Sbjct: 220 ALRREAFDAFMQIEPKQL-----ISDEALYR-EMRLNYSI 253
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 30.1 bits (68), Expect = 1.1
Identities = 22/112 (19%), Positives = 48/112 (42%), Gaps = 8/112 (7%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEV---QAKNKKLQKIYSKYEEVKQDIQDIMDEFNR 59
E ++E+ E+ +++ LE+E + + ++L++ K E + + + + R
Sbjct: 412 EERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVR 471
Query: 60 DRRDLEQSQDELLKDLKLRKLIIENFIPIEELKR--LEQRLVYDEESSQWNI 109
R++ + +L K + E +EEL+R E R + E S
Sbjct: 472 KDREIRARDRRI---ERLEKELEEKKKRVEELERKLAELRKMRKLELSGKGT 520
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 29.8 bits (67), Expect = 1.1
Identities = 29/88 (32%), Positives = 40/88 (45%), Gaps = 18/88 (20%)
Query: 77 LRKLIIENFIPIEELKRLEQRLVYDEESSQWNIVPETNPFYIQKRLVASPQLRRPTTLKA 136
LR+ I + IP EE++ LEQRLV D + + P + L SPQ R P +
Sbjct: 147 LREHIDKLKIPPEEMRELEQRLVKDFQEY---VEPGDD-------LPGSPQRRTPRLSGS 196
Query: 137 REKISQCPTDAGKTRFIGENILTLNFDI 164
+ P +GEN+LT N I
Sbjct: 197 DDDSVLLP--------LGENVLTHNLGI 216
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 29.9 bits (68), Expect = 1.2
Identities = 15/84 (17%), Positives = 41/84 (48%), Gaps = 2/84 (2%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+++EL + EE E+I+ L ++ + + ++ + E++ + + + +E
Sbjct: 338 ELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKR--EQLEKLLETKEKLSEELEELEE 395
Query: 63 DLEQSQDELLKDLKLRKLIIENFI 86
+L++ ++EL K+ + I
Sbjct: 396 ELKELKEELESLYSEGKISVNKTI 419
>gnl|CDD|182093 PRK09819, PRK09819, alpha-mannosidase; Provisional.
Length = 875
Score = 29.9 bits (68), Expect = 1.3
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 15/68 (22%)
Query: 34 KKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLK---------------DLKLR 78
KL +IY + E V +++ ++ + R +L + E + D+K+
Sbjct: 234 DKLNEIYPEREFVISRFENVFEKLEKQRDNLPTLKGEFIDGKYMRVHRSIFSTRMDIKIA 293
Query: 79 KLIIENFI 86
IEN I
Sbjct: 294 NARIENKI 301
>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional.
Length = 361
Score = 29.4 bits (66), Expect = 1.4
Identities = 10/37 (27%), Positives = 21/37 (56%)
Query: 163 DICPNNCKNYQGPKVAPSILSVLQAALQDEADIDVDV 199
++ NC+ QG P ++ ++AA+ E +I V++
Sbjct: 85 EVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVEL 121
>gnl|CDD|222613 pfam14235, DUF4337, Domain of unknown function (DUF4337). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 187 and 201 amino
acids in length. There is a single completely conserved
residue Q that may be functionally important.
Length = 158
Score = 28.7 bits (65), Expect = 1.5
Identities = 12/49 (24%), Positives = 20/49 (40%)
Query: 25 LEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLK 73
LE E A +LQ ++Y++ K + E ++ E D L
Sbjct: 61 LELEAAAPRAELQAKIARYKKEKARYRSEAKELEAKAKEAEAESDHALH 109
>gnl|CDD|220785 pfam10498, IFT57, Intra-flagellar transport protein 57. Eukaryotic
cilia and flagella are specialised organelles found at
the periphery of cells of diverse organisms.
Intra-flagellar transport (IFT) is required for the
assembly and maintenance of eukaryotic cilia and
flagella, and consists of the bidirectional movement of
large protein particles between the base and the distal
tip of the organelle. IFT particles contain multiple
copies of two distinct protein complexes, A and B, which
contain at least 6 and 11 protein subunits. IFT57 is
part of complex B but is not, however, required for the
core subunits to stay associated. This protein is known
as Huntington-interacting protein-1 in humans.
Length = 355
Score = 29.3 bits (66), Expect = 1.5
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
+M Q +S E + L Q++ +K L+KI S+ + + ++ ++ E+ RR
Sbjct: 220 QMHQLKKAISKSLPETKQYLKKLSQDL---SKALEKISSREKHLNNQLEQLVQEYREARR 276
Query: 63 DLEQSQDEL 71
L Q Q++
Sbjct: 277 TLSQVQEKY 285
Score = 28.5 bits (64), Expect = 3.1
Identities = 11/50 (22%), Positives = 28/50 (56%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQD 52
++ QE + + +++ Y+ Q V ++L +I + E+VKQ++++
Sbjct: 266 QLVQEYREARRTLSQVQEKYNQASQGVSELTRELNEISEELEQVKQEMEE 315
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 29.1 bits (66), Expect = 1.8
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 7 ELDKKEESTEEIRGN----YSTLEQEVQAKN---KKLQKIYSKYEEVKQDIQDIMDEFNR 59
+LD+ EE EEI Y LE+EV+AK K + K+ E ++ + ++ E +R
Sbjct: 272 DLDEAEEENEEIEERIDTLYDILEKEVKAKKFVEKNIDKLTDFLEHAREQNKQLLLELDR 331
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 29.2 bits (66), Expect = 1.9
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 10/91 (10%)
Query: 9 DKKEESTEEIRGNYSTLEQEVQAKNKKL-------QKIYSKYEEVKQDIQDIMDEFNRDR 61
D + + L QE+ K KKL Q++ SK E++ ++ E
Sbjct: 200 DCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAE 259
Query: 62 RDLEQSQDELLKDLKLRKLIIENFIPIEELK 92
+ LEQ + K+++ K E ++ L
Sbjct: 260 KKLEQCRGFTFKEIEKLK---EQLKLLQSLT 287
>gnl|CDD|237841 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
Length = 659
Score = 29.0 bits (65), Expect = 2.0
Identities = 18/87 (20%), Positives = 44/87 (50%), Gaps = 16/87 (18%)
Query: 12 EESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDEL 71
EE +EI+ ++ KK + + ++ E ++DEF + +++ +S +E
Sbjct: 356 EEEIKEIKNHF-----------KKKPENFMEWAEKNYLNASLLDEFRKKVKNITKSPEEF 404
Query: 72 LKDLKLRKLIIENFIPIEELKRLEQRL 98
+K+LK + ++ + EEL++ + +
Sbjct: 405 VKELKDKAMVSD-----EELEKYRKEI 426
>gnl|CDD|153341 cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and
Fer (Fes related) tyrosine kinases. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Fes (feline sarcoma), also called
Fps (Fujinami poultry sarcoma), and Fer (Fes related)
are cytoplasmic (or nonreceptor) tyrosine kinases that
play roles in haematopoiesis, inflammation and immunity,
growth factor signaling, cytoskeletal regulation, cell
migration and adhesion, and the regulation of cell-cell
interactions. Although Fes and Fer show redundancy in
their biological functions, they show differences in
their expression patterns. Fer is ubiquitously expressed
while Fes is expressed predominantly in myeloid and
endothelial cells. Fes and Fer contain an N-terminal
F-BAR domain, an SH2 domain, and a C-terminal catalytic
kinase domain. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules. The
F-BAR domain of Fes is critical in its role in
microtubule nucleation and bundling.
Length = 237
Score = 28.9 bits (65), Expect = 2.0
Identities = 10/60 (16%), Positives = 23/60 (38%), Gaps = 7/60 (11%)
Query: 5 KQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDL 64
E++K + Y L ++ +A K ++ K + + D++ + R L
Sbjct: 125 TDEVEKLKSE-------YQKLLEDYKAAKSKFEEAVVKGGRGGRKLDKARDKYQKACRKL 177
>gnl|CDD|133406 cd04779, HTH_MerR-like_sg4, Helix-Turn-Helix DNA binding domain of
putative transcription regulators from the MerR
superfamily. Putative helix-turn-helix (HTH) MerR-like
transcription regulators (subgroup 4). Based on sequence
similarity, these proteins are predicted to function as
transcription regulators that mediate responses to
stress in eubacteria. They belong to the MerR
superfamily of transcription regulators that promote
transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of two distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 134
Score = 27.9 bits (62), Expect = 2.5
Identities = 10/65 (15%), Positives = 33/65 (50%)
Query: 27 QEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENFI 86
E++ + +++Q+ + EV Q++Q + D+ + L+Q + + + +++ + +
Sbjct: 60 AEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQLKPIASQTDRAQRMKMTKEL 119
Query: 87 PIEEL 91
+ L
Sbjct: 120 SQQVL 124
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.4 bits (64), Expect = 3.1
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 8 LDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEE 45
LDKKEE+ E+ S E+ + K ++L+++ ++ E
Sbjct: 99 LDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQRE 136
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.5 bits (64), Expect = 3.1
Identities = 27/110 (24%), Positives = 58/110 (52%), Gaps = 17/110 (15%)
Query: 2 IEMKQELDKKEESTEEIRGNYSTL----EQEVQAKNKKLQKIYSKYEEVK---QDIQDIM 54
E++++LD+ EE E+ L +E++ + K+L+ Y++Y E+K ++++
Sbjct: 559 AELEKKLDELEEELAELLKELEELGFESVEELEERLKELEPFYNEYLELKDAEKELEREE 618
Query: 55 DEFNRDRRDLEQSQDEL-LKDLKLRKLIIENFIPIEELKRLEQRLVYDEE 103
E + +L+++ +EL + +L +L E +EEL++ Y EE
Sbjct: 619 KELKKLEEELDKAFEELAETEKRLEELRKE----LEELEKK-----YSEE 659
Score = 27.3 bits (61), Expect = 7.4
Identities = 22/97 (22%), Positives = 57/97 (58%), Gaps = 2/97 (2%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
+ +EL++ +E EE+ +LE + +K++++ + EE+K++I++ ++E ++ +
Sbjct: 228 KEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEE-LEEKVKELK 286
Query: 63 DLEQSQDELLKDLKLRKLIIENFIPIE-ELKRLEQRL 98
+L++ +E +K + + ++ IE L RLE+ +
Sbjct: 287 ELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEI 323
Score = 27.3 bits (61), Expect = 8.1
Identities = 12/80 (15%), Positives = 33/80 (41%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ E +E + E+ ++ + K+L++ + EE+K+ ++++
Sbjct: 298 LSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEEL 357
Query: 61 RRDLEQSQDELLKDLKLRKL 80
E ++ K +L +L
Sbjct: 358 EERHELYEEAKAKKEELERL 377
>gnl|CDD|205513 pfam13333, rve_2, Integrase core domain.
Length = 52
Score = 25.9 bits (58), Expect = 3.3
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 38 KIYSKYEEVKQDIQDIMDEFNRDRR 62
K + EE+KQ I + ++ +N R
Sbjct: 15 KTFKTLEELKQAIFEYIEYYNNKRL 39
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 28.3 bits (64), Expect = 3.3
Identities = 25/95 (26%), Positives = 41/95 (43%), Gaps = 10/95 (10%)
Query: 8 LDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQS 67
D E E + Y E Q +KL I E + ++++++ E ++ L S
Sbjct: 138 NDDGSELEERLTPVYPLTEGLKQKTLRKL--IQQALEVLPSELEELLPEELLEKYGLP-S 194
Query: 68 QDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDE 102
DE L+ L K E+LKR +RL ++E
Sbjct: 195 LDEALRTLHFPK-------DEEDLKRARRRLAFEE 222
>gnl|CDD|213617 TIGR01417, PTS_I_fam, phosphoenolpyruvate-protein
phosphotransferase. This model recognizes a distinct
clade of phophoenolpyruvate (PEP)-dependent enzymes.
Most members are known or deduced to function as the
phosphoenolpyruvate-protein phosphotransferase (or
enzyme I) of PTS sugar transport systems. However, some
species with both a member of this family and a homolog
of the phosphocarrier protein HPr lack a IIC component
able to serve as a permease. An HPr homolog designated
NPr has been implicated in the regulation of nitrogen
assimilation, which demonstrates that not all
phosphotransferase system components are associated
directly with PTS transport.
Length = 565
Score = 28.2 bits (63), Expect = 3.4
Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 8 LDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQS 67
L K + + + + S ++QE+ K K E +K F +++ + ++
Sbjct: 18 LKKPDLVIDRKKISASQVDQEISRFLKARAKAKEDLETIKTKA---GKTFGQEKAAIFEA 74
Query: 68 QDELLKDLKLRKLIIE 83
+L+D +L + +IE
Sbjct: 75 HILILEDPELTEEVIE 90
>gnl|CDD|212167 cd11653, rap1_RCT, C-terminal domain of RAP1 recruits proteins to
telomeres. The RAP1 (repressor activator protein 1)
C-terminal domain (RCT) mediates interactions with
other proteins such as TRF2 (human), Rif1, Rif2, Sir3,
Sir4 (Saccharomyces cerevisiae), and Taz1
(Schizosaccharomyces pombe) at telomeres and other
loci. RAP1, identified in budding yeast as
repressor/activator protein 1, is a well-conserved
telomere binding protein, also found in fission yeast
and mammals. In Saccharomyces cerevisiae, RAP1 directly
binds DNA and is involved in transcriptional
activation, gene silencing, as well as binding at
numerous sites at each telemore, where it functions in
telomere length regulation, telomeric position effect
gene silencing and telomere end protection. Human RAP1
apparently does not bind telomeric DNA directly, but
binds telomere repeat binding factor 2 (TRF2) via the
RCT. RAP1 might act by suppressing nonhomologous
end-joining. Yeast RAP1 has two myb-type DNA binding
modules, and an RCT domain that recruits Sir proteins 3
and 4 (Sir3, Sir4) for gene silencing, and Rif1 and
Rif2 for telomere length maintenance.
Schizosaccharomyces pombe RAP1 (spRap1), like human
RAP1, lacks direct DNA-binding activity and is
localized to telomeres via Taz1, an ortholog of TRF1
and TRF2. The S. pompe RCT resembles the first 3-helix
bundle of the yeast and human RCT forms, but is not
included in this larger model.
Length = 100
Score = 26.9 bits (60), Expect = 3.5
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 44 EEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKL 77
E+ ++ +QD+ DE + Q+ + L +
Sbjct: 7 EQAEKLVQDLDDEIGIRLVTVTQALLKASGCLSM 40
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 28.3 bits (64), Expect = 3.7
Identities = 16/69 (23%), Positives = 39/69 (56%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
++++ D+ E E YS L++E++ K+L++I + E++ + +Q + + R
Sbjct: 359 SLEKQYDEITERIAEQEIAYSELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEARE 418
Query: 63 DLEQSQDEL 71
LE+ +++L
Sbjct: 419 KLERYRNKL 427
Score = 27.9 bits (63), Expect = 4.7
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 10/94 (10%)
Query: 7 ELDKKEESTEEIRGN----YSTLEQEVQAKN---KKLQKIYSKYEEVKQDIQDIMDEFNR 59
+LD+ EE EEI+ Y LE+EV+A+ K + E K+ +++ +E +R
Sbjct: 276 DLDEAEEKNEEIQERIDQLYDILEREVKARKYVEKNSDTLPDFLEHAKEQNKELKEEIDR 335
Query: 60 DRRDLEQSQDELLKDLKLRK---LIIENFIPIEE 90
++ ++ EL +L K + + + I E
Sbjct: 336 VKQSYTLNESELESVRQLEKQLESLEKQYDEITE 369
>gnl|CDD|237255 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 28.2 bits (63), Expect = 4.0
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 34 KKLQKIY-SKYEEVKQDIQDIMDEFNRDRRDLEQSQDELL--KDLKLRKLIIENFIPIE- 89
K +KI+ SK+E+ + IQ I+D N + L D+ L K ++L+ + PIE
Sbjct: 3 KIFEKIFGSKHEKDIKKIQPIIDRINEIQASLASLSDDALREKGMELKSRVRGALEPIEQ 62
Query: 90 ELKRLEQRL 98
+ K LE++L
Sbjct: 63 KKKDLEKKL 71
>gnl|CDD|214016 cd12923, iSH2_PI3K_IA_R, Inter-Src homology 2 (iSH2) helical
domain of Class IA Phosphoinositide 3-kinase Regulatory
subunits. PI3Ks catalyze the transfer of the
gamma-phosphoryl group from ATP to the 3-hydroxyl of
the inositol ring of D-myo-phosphatidylinositol
(PtdIns) or its derivatives. They play an important
role in a variety of fundamental cellular processes,
including cell motility, the Ras pathway, vesicle
trafficking and secretion, immune cell activation, and
apoptosis. They are classified according to their
substrate specificity, regulation, and domain
structure. Class IA PI3Ks are heterodimers of a p110
catalytic (C) subunit and a p85-related regulatory (R)
subunit. The R subunit down-regulates PI3K basal
activity, stabilizes the C subunit, and plays a role in
the activation downstream of tyrosine kinases. All R
subunits contain two SH2 domains that flank an
intervening helical domain (iSH2), which binds to the
N-terminal adaptor-binding domain (ABD) of the
catalytic subunit. In vertebrates, there are three
genes (PIK3R1, PIK3R2, and PIK3R3) that encode for
different Class IA PI3K R subunits.
Length = 152
Score = 27.2 bits (61), Expect = 4.3
Identities = 9/39 (23%), Positives = 22/39 (56%)
Query: 13 ESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQ 51
+ E++ + +E K+++ ++Y KY ++ Q+IQ
Sbjct: 1 DDVEKLAKKLKEINKEYLDKSREYDELYEKYNKLSQEIQ 39
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 27.7 bits (62), Expect = 4.5
Identities = 12/61 (19%), Positives = 30/61 (49%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
K +L+K + + LE+E++ L++ +YEE+ + +++ + F+ +R
Sbjct: 128 SKKAQLEKLKAAPGIKPAKVEELEEELEEAESALEEARKRYEEISERLKEELKRFHEERA 187
Query: 63 D 63
Sbjct: 188 R 188
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 28.1 bits (63), Expect = 4.6
Identities = 14/64 (21%), Positives = 29/64 (45%)
Query: 7 ELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
EL E + + E ++KKL ++ +K KQ + ++D+ + + +E+
Sbjct: 310 ELQHSLEKLDTAIDELEEIMDEFNEQSKKLLELKNKISTNKQSLITLVDKAKKVKAAIEE 369
Query: 67 SQDE 70
Q E
Sbjct: 370 LQAE 373
>gnl|CDD|217962 pfam04201, TPD52, Tumour protein D52 family. The hD52 gene was
originally identified through its elevated expression
level in human breast carcinoma. Cloning of D52
homologues from other species has indicated that D52
may play roles in calcium-mediated signal transduction
and cell proliferation. Two human homologues of hD52,
hD53 and hD54, have also been identified, demonstrating
the existence of a novel gene/protein family. These
proteins have an amino terminal coiled-coil that allows
members to form homo- and heterodimers with each other.
Length = 162
Score = 27.2 bits (60), Expect = 4.6
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 12/53 (22%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSK-----YEEVKQDI 50
E++ EL K E EEI STL Q + AK K L ++ K E+KQ+I
Sbjct: 33 ELRTELAKLE---EEI----STLRQVLAAKEKHLAELKRKLGLTPLSELKQNI 78
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 27.9 bits (63), Expect = 4.7
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 27 QEVQAKNKKLQKIYSKYEEVKQDIQDIMD--EFNRDRRDLEQSQDELLKDLKLRKLIIEN 84
Q+V + L+ EE++Q + D+ + E + D E++ E +LK + +
Sbjct: 52 QKVTKELSSLKAKLDTLEELRQRLDDLEELLELAEEEDD-EETLAEAEAELKALEKKLAA 110
Query: 85 FIPIEELKRL 94
EL+RL
Sbjct: 111 L----ELERL 116
>gnl|CDD|234539 TIGR04317, W_rSAM_matur, tungsten cofactor oxidoreducase radical
SAM maturase. Members of this family are radical SAM
enzymes involved in the maturation of tungsten
(W)-containing cofactors in the enzymes aldehyde
ferredoxin oxidoreductase, formaldehyde ferredoxin
oxidoreductase, and others, and tend to be encoded by an
adjacent gene.
Length = 349
Score = 27.7 bits (62), Expect = 4.8
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 34 KKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ--SQDELLKDLKLRKLIIENFIPIEEL 91
+ L+K+Y + D + EF + + ++ EL + L + +I+ N +P E
Sbjct: 131 ENLKKLYEIKIKKGSDKPHVGIEFVATKENYKELPELVELARKLGVSSIIVSNLLPYTE- 189
Query: 92 KRLEQRLVYDEESSQ 106
++YD
Sbjct: 190 -EYIDEILYDGPGEL 203
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 27.7 bits (62), Expect = 4.9
Identities = 12/63 (19%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 6 QELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDI-------MDEFN 58
EL KK+ E+++ T ++++ + +L++ + E+K++ +++ ++ F
Sbjct: 122 SELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEVSELIKSELERFE 181
Query: 59 RDR 61
R+R
Sbjct: 182 RER 184
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 27.2 bits (61), Expect = 5.0
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 27 QEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENFI 86
Q + +L+K+ + EE+KQ I ++ + + ++ E++++ +L++L E
Sbjct: 62 QALNKLKTRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKE--- 118
Query: 87 PIEELKR-LEQRLVYDEES 104
+++LK LE+ D E
Sbjct: 119 -LKKLKAELEKYEKNDPER 136
>gnl|CDD|224340 COG1422, COG1422, Predicted membrane protein [Function unknown].
Length = 201
Score = 27.3 bits (61), Expect = 5.1
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 5/45 (11%)
Query: 36 LQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKL 80
LQK+ E++K+ +Q +M EF ++ R+ ++S D KL+KL
Sbjct: 64 LQKLLIDQEKMKE-LQKMMKEFQKEFREAQESGD----MKKLKKL 103
>gnl|CDD|112704 pfam03904, DUF334, Domain of unknown function (DUF334).
Staphylococcus aureus plasmid proteins with no
characterized function.
Length = 229
Score = 27.7 bits (61), Expect = 5.1
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQ---DIQDIMDEFNR 59
E+K+ D +E+ + I+ ++ Q K KK+ + + K D +DI DE +
Sbjct: 60 EIKENQDIREKELKAIKSELKEATEDFQDKGKKIHNDFVDLLQEKLKHVDAEDIEDELGK 119
Query: 60 DRRDLEQSQDELLKDLK 76
D + + D +L+++K
Sbjct: 120 DIYGVREEIDRMLQEVK 136
>gnl|CDD|153331 cd07647, F-BAR_PSTPIP, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine
Phosphatase-Interacting Proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Vetebrates contain two
Proline-Serine-Threonine Phosphatase-Interacting
Proteins (PSTPIPs), PSTPIP1 and PSTPIP2. PSTPIPs are
mainly expressed in hematopoietic cells and are involved
in the regulation of cell adhesion and motility.
Mutations in PSTPIPs have been shown to cause
autoinflammatory disorders. PSTPIP1 contains an
N-terminal F-BAR domain, PEST motifs, and a C-terminal
SH3 domain, while PSTPIP2 contains only the N-terminal
F-BAR domain. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 239
Score = 27.4 bits (61), Expect = 5.3
Identities = 14/64 (21%), Positives = 34/64 (53%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ +K D + TE + + L Q ++ + +KL++ K +E ++ +DIM ++
Sbjct: 55 IGTLKSSWDSLRKETENVANAHIQLAQSLREEAEKLEEFREKQKEERKKTEDIMKRSQKN 114
Query: 61 RRDL 64
+++L
Sbjct: 115 KKEL 118
>gnl|CDD|180700 PRK06800, fliH, flagellar assembly protein H; Validated.
Length = 228
Score = 27.5 bits (61), Expect = 5.6
Identities = 13/70 (18%), Positives = 34/70 (48%)
Query: 2 IEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDR 61
E++++ ++ + + + L QE Q ++ Q++ + E+ ++ +Q M E R
Sbjct: 34 EEIQKDHEELLAQQKSLHKELNQLRQEQQKLERERQQLLADREQFQEHVQQQMKEIEAAR 93
Query: 62 RDLEQSQDEL 71
+ ++ Q E
Sbjct: 94 QQFQKEQQET 103
>gnl|CDD|144876 pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain. These
proteins contain several 22 residue repeats which form
a pair of alpha helices. This family includes:
Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein
E.
Length = 191
Score = 27.2 bits (61), Expect = 5.6
Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 15/99 (15%)
Query: 1 MIEMKQELDKKEES----TEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDE 56
+ E+ ++ +E +E L +E +A ++LQK E+V+ +Q +DE
Sbjct: 7 LDELNSYAEELQEQLGPYAQEFWAR---LSKETEALREELQK---DLEDVRARLQPYLDE 60
Query: 57 FNRDRRDLEQSQDELLKDLK--LRKLIIENFIPIEELKR 93
+ + Q+ +EL + L +L EEL+R
Sbjct: 61 L---KAKVGQNLEELRQRLAPYAEELRKRLNRDAEELRR 96
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 28.0 bits (62), Expect = 5.7
Identities = 10/39 (25%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 24 TLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
++ + V + LQK++++++ + Q++Q+ E+ R+RR
Sbjct: 977 SISEYVSNPQQLLQKVFAEFQ-IPQELQNTYFEYARNRR 1014
>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein
[Function unknown].
Length = 294
Score = 27.3 bits (61), Expect = 5.9
Identities = 24/115 (20%), Positives = 60/115 (52%), Gaps = 7/115 (6%)
Query: 2 IEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFN--R 59
++K+E+++ +E +E+R S L ++ N K++++ K +E++++ +I +E +
Sbjct: 16 KQLKEEIEELKEKRDELRKEASELAEKRDELNAKVRELREKAQELREERDEINEEVQELK 75
Query: 60 DRRD-----LEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVYDEESSQWNI 109
++RD L++ + E + + R I+ L+R +RL +++S
Sbjct: 76 EKRDEINAKLQELRKEYRELKEKRNEFNLGGRSIKSLEREIERLEKKQQTSVLTP 130
>gnl|CDD|237763 PRK14603, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 197
Score = 27.1 bits (60), Expect = 5.9
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 174 GPKVAPSILSVLQAALQDEADIDVDVKSTAS 204
GPK+A ++LS L AL A ++ D + S
Sbjct: 81 GPKLALALLSALPPALLARALLEGDARLLTS 111
>gnl|CDD|222563 pfam14131, DUF4298, Domain of unknown function (DUF4298). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
eukaryotes. Proteins in this family are typically
between 94 and 105 amino acids in length. There are two
completely conserved residues (Y and D) that may be
functionally important.
Length = 90
Score = 26.1 bits (58), Expect = 6.3
Identities = 4/32 (12%), Positives = 20/32 (62%)
Query: 35 KLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQ 66
++++IY+++ E+ +++ +++ + D +
Sbjct: 4 EMEEIYNRFSELLAKLEEALEQLKEAQEDYRE 35
>gnl|CDD|218651 pfam05600, DUF773, Protein of unknown function (DUF773). This
family contains several eukaryotic sequences which are
thought to be CDK5 activator-binding proteins, however,
the function of this family is unknown.
Length = 506
Score = 27.7 bits (62), Expect = 6.4
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 15/80 (18%)
Query: 6 QELDKKEE----STEEIRGNYST-----------LEQEVQAKNKKLQKIYSKYEEVKQDI 50
QEL++KEE S + R Y + QE+ A K L + K E +
Sbjct: 141 QELERKEEDCKRSAADSREQYYAACKQLGIKGENVRQELLALVKDLPSVLEKIGEDIAPL 200
Query: 51 QDIMDEFNRDRRDLEQSQDE 70
++ + + S ++
Sbjct: 201 SKAIELYQAFVGFVCDSSEK 220
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 27.6 bits (62), Expect = 6.5
Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 34 KKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKR 93
+ L++ + EE ++++ +DE D LE+ ++ L L+ L + + IE+L
Sbjct: 269 ELLEEALYELEEASEELRAYLDELEFDPNRLEEVEERL---FALKSLARKYGVTIEDLLE 325
Query: 94 LEQRLVYD 101
++ +
Sbjct: 326 YLDKIKEE 333
>gnl|CDD|238244 cd00429, RPE, Ribulose-5-phosphate 3-epimerase (RPE). This enzyme
catalyses the interconversion of D-ribulose 5-phosphate
(Ru5P) into D-xylulose 5-phosphate, as part of the
Calvin cycle (reductive pentose phosphate pathway) in
chloroplasts and in the oxidative pentose phosphate
pathway. In the Calvin cycle Ru5P is phosphorylated by
phosphoribulose kinase to ribulose-1,5-bisphosphate,
which in turn is used by RubisCO
(ribulose-1,5-bisphosphate carboxylase/oxygenase) to
incorporate CO2 as the central step in carbohydrate
synthesis.
Length = 211
Score = 27.1 bits (61), Expect = 6.6
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 9/33 (27%)
Query: 176 KVAPSILSVLQAALQDE------ADID---VDV 199
K+APSILS A L +E A D +DV
Sbjct: 1 KIAPSILSADFANLGEELKRLEEAGADWIHIDV 33
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This
family includes outer membrane proteins such as OmpH
among others. Skp (OmpH) has been characterized as a
molecular chaperone that interacts with unfolded
proteins as they emerge in the periplasm from the Sec
translocation machinery.
Length = 140
Score = 26.8 bits (60), Expect = 6.7
Identities = 12/63 (19%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 22 YSTLEQEVQAKNKKLQKIYSKYEE-----VKQDIQDIMDEFNRDRRDLEQSQDELLKDLK 76
+ + E++ K+LQK+ K ++ + + E + ++ ++ Q +L +DL+
Sbjct: 27 FKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQKKVQEFQRKQQKLQQDLQ 86
Query: 77 LRK 79
R+
Sbjct: 87 KRQ 89
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 27.4 bits (61), Expect = 6.7
Identities = 15/58 (25%), Positives = 28/58 (48%)
Query: 11 KEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQ 68
+++S E GNYS+ E + + + Q +Y +E +Q +D F +Q+Q
Sbjct: 220 EQQSLFEYTGNYSSFEVQRATRLAQQQAMYESQQERVAHLQSYIDRFRAKATKAKQAQ 277
>gnl|CDD|131391 TIGR02338, gimC_beta, prefoldin, beta subunit, archaeal.
Chaperonins are cytosolic, ATP-dependent molecular
chaperones, with a conserved toroidal architecture, that
assist in the folding of nascent and/or denatured
polypeptide chains. The group I chaperonin system
consists of GroEL and GroES, and is found (usually) in
bacteria and organelles of bacterial origin. The group
II chaperonin system, called the thermosome in Archaea
and TRiC or CCT in the Eukaryota, is structurally
similar but only distantly related. Prefoldin, also
called GimC, is a complex in Archaea and Eukaryota, that
works with group II chaperonins. Members of this protein
family are the archaeal clade of the beta class of
prefoldin subunit. Closely related, but outside the
scope of this family are the eukaryotic beta-class
prefoldin subunits, Gim-1,3,4 and 6. The alpha class
prefoldin subunits are more distantly related.
Length = 110
Score = 26.2 bits (58), Expect = 7.1
Identities = 11/45 (24%), Positives = 28/45 (62%)
Query: 10 KKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIM 54
KEE+ +E++ TLE V+ ++ +++ + +E+++ IQ+ +
Sbjct: 64 DKEEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQEAL 108
>gnl|CDD|237560 PRK13922, PRK13922, rod shape-determining protein MreC;
Provisional.
Length = 276
Score = 27.3 bits (61), Expect = 7.1
Identities = 11/55 (20%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 17 EIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDEL 71
+ + ++L +++ +N++L+K + E Q+++ + E N R+L ++ L
Sbjct: 63 GVFESLASL-FDLREENEELKKELLELESRLQELEQLEAE-NARLRELLNLKESL 115
>gnl|CDD|238345 cd00632, Prefoldin_beta, Prefoldin beta; Prefoldin is a hexameric
molecular chaperone complex, composed of two
evolutionarily related subunits (alpha and beta), which
are found in both eukaryotes and archaea. Prefoldin
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The hexameric
structure consists of a double beta barrel assembly with
six protruding coiled-coils. The alpha prefoldin
subunits have two beta hairpin structures while the beta
prefoldin subunits (this CD) have only one hairpin that
is most similar to the second hairpin of the alpha
subunit. The prefoldin hexamer consists of two alpha and
four beta subunits and is assembled from the beta
hairpins of all six subunits. The alpha subunits
initially dimerize providing a structural nucleus for
the assembly of the beta subunits. In archaea, there is
usually only one gene for each subunit while in
eukaryotes there two or more paralogous genes encoding
each subunit adding heterogeneity to the structure of
the hexamer.
Length = 105
Score = 26.2 bits (58), Expect = 7.4
Identities = 10/42 (23%), Positives = 25/42 (59%)
Query: 10 KKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQ 51
+KEE+ E++ T+E ++ ++ + + K +E+++ IQ
Sbjct: 60 EKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKIQ 101
>gnl|CDD|234309 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase. This family of
alanyl-tRNA synthetases is limited to the archaea, and
is a subset of those sequences identified by the model
pfam07973 covering the second additional domain (SAD) of
alanyl and threonyl tRNA synthetases.
Length = 902
Score = 27.3 bits (61), Expect = 7.5
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 11/69 (15%)
Query: 34 KKLQKIYSKYEEVKQDIQDIMD-EFNRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELK 92
++L+KIY + +E K I DI+D E + R LE+ + + + LK +K IP+++L
Sbjct: 386 EELKKIYPELKENKDYILDILDLEEEKYRETLERGRRIVERLLKTKKE-----IPLDDLI 440
Query: 93 RLEQRLVYD 101
L YD
Sbjct: 441 EL-----YD 444
>gnl|CDD|193608 cd09641, Cas3''_I, CRISPR/Cas system-associated protein Cas3''.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
HD-like nuclease, specifically digesting double-stranded
oligonucleotides and preferably cleaving at G:C pairs;
signature gene for Type I.
Length = 200
Score = 26.9 bits (59), Expect = 7.5
Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 42 KYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLVY 100
+K+ ++++ DE E+ +ELL +L L++ + L RL++
Sbjct: 126 DESALKERLEEL-DEEKLLLELWEEELEELLDELLKELLLLLLPELLSFELYLLLRLLF 183
>gnl|CDD|187784 cd09653, Csa5_I-A, CRISPR/Cas system-associated protein Csa5.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Predicted transcriptional regulator of CRISPR/Cas
system; contains DNA binding HTH domain; also known as
Csa5 family.
Length = 97
Score = 26.0 bits (57), Expect = 7.7
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 18 IRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRR 62
E+ + K+ +KI Y ++++D + E D
Sbjct: 37 GIETAMIDEKGYRYAEKEGRKILVGYLPTDKEVEDFLREVREDIE 81
>gnl|CDD|227744 COG5457, COG5457, Uncharacterized conserved small protein
[Function unknown].
Length = 63
Score = 25.4 bits (56), Expect = 7.7
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 55 DEFNRDRRDLEQSQDELLKDLKLRKLIIEN 84
+ R RR+L + D LL D+ + + IE
Sbjct: 26 RRYRRTRRELLRLSDHLLSDIGISRADIEA 55
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 27.4 bits (61), Expect = 7.8
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 23 STLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLKLRKLI- 81
+++E+ A KK+++ + ++++ ++ + E L ++ D+L KLRK I
Sbjct: 41 KQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDL---KKLRKQIA 97
Query: 82 -IENFIPIEELKRLEQRLVYDE 102
+ + E++ EQR E
Sbjct: 98 DLNARLNALEVQEREQRRRLAE 119
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 320
Score = 27.0 bits (60), Expect = 8.1
Identities = 16/96 (16%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 1 MIEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRD 60
+ E+ +DK ++ + N + + + KL I+++ ++++ N
Sbjct: 151 IYEIDNFIDKT--LSKILDDNIVFQDNLEKNIDDKLSNIFNEK---LSNLKNEKISIN-- 203
Query: 61 RRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQ 96
++ +E+ D K K + N I +E +K
Sbjct: 204 -EKIKSILNEINPDSKFEKKLDLNLIKLEIVKSNSD 238
>gnl|CDD|220133 pfam09177, Syntaxin-6_N, Syntaxin 6, N-terminal. Members of this
family, which are found in the amino terminus of
various SNARE proteins, adopt a structure consisting of
an antiparallel three-helix bundle. Their exact
function has not been determined, though it is known
that they regulate the SNARE motif, as well as mediate
various protein-protein interactions involved in
membrane-transport.
Length = 96
Score = 25.7 bits (57), Expect = 8.4
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 26 EQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLK 76
+ EVQ KL+ +Y + ++ D E + ++L + + + DL+
Sbjct: 7 KDEVQKSIDKLRSLYRSWLRIRSDSNS--PELDELTKELRNALESIEWDLE 55
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 26.9 bits (60), Expect = 8.4
Identities = 19/128 (14%), Positives = 46/128 (35%), Gaps = 15/128 (11%)
Query: 2 IEMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDR 61
+ + +L+K +E + S +E+ +N+ ++I + K I++I E +
Sbjct: 23 LSVDIDLEKLIALDDERKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELK 82
Query: 62 R---DLEQSQDELLKDLKLRKLIIENFI------------PIEELKRLEQRLVYDEESSQ 106
+L + L +L+ + L I N +E + + +
Sbjct: 83 EELTELSAALKALEAELQDKLLSIPNIPHESVPVGKDEEDNLEVKRWGTPPVFDFKPKPH 142
Query: 107 WNIVPETN 114
W + +
Sbjct: 143 WELGEKLG 150
>gnl|CDD|189016 cd09609, M3B_PepF_4, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 586
Score = 27.2 bits (61), Expect = 8.5
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 11/71 (15%)
Query: 20 GNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNR-----DRRDLEQSQDEL--- 71
+Y++L Q + + Q +K++ + I + F D + LE+ +EL
Sbjct: 68 SHYASLPQSTDGTDPENQARAAKFDSLAAKINAKLSFFESELLALDEKILEEVIEELPEY 127
Query: 72 ---LKDLKLRK 79
L+DL +K
Sbjct: 128 AAYLEDLLRKK 138
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 27.0 bits (60), Expect = 8.8
Identities = 12/79 (15%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 6 QELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLE 65
++ ++ E++ ++ E+++ + ++++I SK +E++++I D+ + + L+
Sbjct: 31 DKIQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEI----DQSKAEIKKLQ 86
Query: 66 QSQDELLKDLKLRKLIIEN 84
+ EL +++ R+ +++
Sbjct: 87 KEIAELKENIVERQELLKK 105
>gnl|CDD|237426 PRK13558, PRK13558, bacterio-opsin activator; Provisional.
Length = 665
Score = 27.1 bits (60), Expect = 9.0
Identities = 9/49 (18%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 168 NCKNYQGPKVAPSILSVLQAALQDEADIDVDVKSTASKKIHRANKTPLY 216
NC+ QG ++ L+ A+ +E V++++ +R + + +
Sbjct: 195 NCRFLQGEDTNEERVAELREAIDEERPTSVELRN------YRKDGSTFW 237
>gnl|CDD|226371 COG3853, TelA, Uncharacterized protein involved in tellurite
resistance [Inorganic ion transport and metabolism].
Length = 386
Score = 27.0 bits (60), Expect = 9.4
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 34 KKLQKIYSKYEEVKQDIQDIMDEFNRDRRDLEQSQDELLKDLK-LRKLIIENFIPIEEL 91
+Q+I+SKY+ + I I++ L + +DEL +D K L L +N E L
Sbjct: 130 SSIQEIFSKYQTIGAQIDRIIES-------LSKGKDELTRDNKMLELLYEKNREYFEHL 181
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 27.0 bits (60), Expect = 9.4
Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 12/100 (12%)
Query: 3 EMKQELDKKEESTEEIRGNYSTLEQEVQAKNKKLQKIYSKYE---EVKQDIQDIMDEFNR 59
E+K+++++ E + E I EV+ +Q+ + + E + ++ + E
Sbjct: 775 ELKRQIEELETTIERIAVR----RPEVREYRAFMQETWLHRDSLREERPNLAIQLRELES 830
Query: 60 DRRDLEQSQDELLKDLKLRKLIIENFIPIEELKRLEQRLV 99
+L+Q L+KD KLR+ +E +E K LE++L
Sbjct: 831 SAEELQQELTRLIKDTKLRRKKLE-----QERKALEKQLD 865
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.313 0.132 0.365
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,490,388
Number of extensions: 1115052
Number of successful extensions: 2206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1991
Number of HSP's successfully gapped: 489
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.6 bits)