RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013474
(442 letters)
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 56.8 bits (138), Expect = 1e-09
Identities = 20/71 (28%), Positives = 35/71 (49%)
Query: 372 RNALTEKKRRPLYRKGFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGP 431
+ + K++D+NR KV KGG+ +++A++ G+ +G VGF K
Sbjct: 8 IEFKSGLPIKEPEVDELLEKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRVGFGIGKAK 67
Query: 432 AVPIALQKVTW 442
VP A++K
Sbjct: 68 EVPEAIRKAIE 78
>gnl|CDD|144065 pfam00333, Ribosomal_S5, Ribosomal protein S5, N-terminal domain.
Length = 67
Score = 53.4 bits (129), Expect = 2e-09
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 391 KLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442
K++ +NR KVTKGG+ + A++ G+ +G VG + K VP A++K
Sbjct: 5 KVLVINRVQKVTKGGRRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIE 56
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 52.4 bits (127), Expect = 4e-08
Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 391 KLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQK 439
K++ +NR KV KGG+ ++A++ G+ G VGF K VP A++K
Sbjct: 16 KVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRK 64
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle
type. This model finds chloroplast ribosomal protein S5
as well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included
in this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 51.1 bits (123), Expect = 8e-08
Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 391 KLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQK 439
+LI VNR KV KGG+ ++A++ G+ G VGF K VP A++K
Sbjct: 5 RLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKK 53
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 46.1 bits (110), Expect = 1e-05
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 387 GFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQK 439
+ +++D+N ++T G+ V++ ++ GN G VG + K V A++K
Sbjct: 49 DLEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRK 101
>gnl|CDD|233235 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal
type)/S2(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S2 as well as archaeal
ribosomal protein S5 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 212
Score = 42.8 bits (101), Expect = 1e-04
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 389 DVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQK 439
+ +++DV+ ++T G+ ++ A + GN G VG K V A++K
Sbjct: 51 EEEVLDVSLVQRMTDSGRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPAIRK 101
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 42.0 bits (99), Expect = 6e-04
Identities = 52/276 (18%), Positives = 110/276 (39%), Gaps = 36/276 (13%)
Query: 107 QDLLAEVEREKGR-EREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNL 165
+DLL E+E++ + ER+A K + + + E + + +++L KE + +L+
Sbjct: 192 EDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAK-LKELRKELEELEEELSR 250
Query: 166 YEEPTDSDSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETP--DEAFKWMNKI 223
EE + + + + +K+ + K L+ E +E + +I
Sbjct: 251 LEE-------------ELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEI 297
Query: 224 DKFEQKHFPLRHEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNY 283
++ E + + + EL N L+E E + + + ++ L E + +
Sbjct: 298 EELEGE---ISLLRERLEELENELEELEERLEELKEKIEALKEELEERETL--------- 345
Query: 284 GVIRHEQAGPNVDAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKL 343
+ + A +E + L + ++ EE F+ ++E L L I +L
Sbjct: 346 -----LEELEQLLAELEEAKEELEEKL-SALLEELEELFEALREELAELEAELAEIRNEL 399
Query: 344 EEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKK 379
EE E++ + + L E + DL EE L +
Sbjct: 400 EELKREIESLEERLER-LSERLEDLKEELKELEAEL 434
Score = 30.1 bits (68), Expect = 2.8
Identities = 23/60 (38%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 319 EEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEK 378
EEE ++++E+ D L E L ++K+LEE EL+ +K + LE+E+++L EE+ L E+
Sbjct: 834 EEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEE-LEDELKELEEEKEELEEE 892
Score = 29.3 bits (66), Expect = 4.9
Identities = 54/277 (19%), Positives = 105/277 (37%), Gaps = 60/277 (21%)
Query: 107 QDLLAEVEREKGREREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNLY 166
+ L E+ + E R++ + +++ E + LE+E + L
Sbjct: 691 KSLKNELRSLEDLLEELRRQLEELERQLEELKRE--------LAALEEELEQLQSRLEEL 742
Query: 167 EEPTDSDSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKF 226
EE + +E +E Q++ + +E L + K +I++
Sbjct: 743 EEELEELEEELEEL-------------QERLEELEEEL-----ESLEEALAKLKEEIEEL 784
Query: 227 EQKHFPLRHEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGVI 286
E+K L+ E + E + + + L+ R RL +
Sbjct: 785 EEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQ---------------- 828
Query: 287 RHEQAGPNVDAVENAEMDEEKRLLQGGVD--DDDEEEFDDMKERDDILLERLNAIDKKLE 344
E E++EE L+ +D +++ EE + E LE L A ++LE
Sbjct: 829 ------------EIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELE 876
Query: 345 EKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRR 381
++L EL+ ++ + LEEE+R+L E L E+ +
Sbjct: 877 DELKELE----EEKEELEEELRELESELAELKEEIEK 909
Score = 28.9 bits (65), Expect = 6.3
Identities = 52/279 (18%), Positives = 113/279 (40%), Gaps = 41/279 (14%)
Query: 107 QDLLAEVEREKGREREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNLY 166
++ + E+E ++ +E + E EE+ ++ LE+E
Sbjct: 778 KEEIEELEEKRQALQEELE-----------ELEEELEEAERRLDALERELESLEQRRERL 826
Query: 167 EEPTDSDSDEDDERFSR-DAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDK 225
E+ + +E +E + D + + + +K+ + KE L+ + E ++ +
Sbjct: 827 EQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELED-----ELKE 881
Query: 226 FEQKHFPLRHEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGV 285
E++ L E R EL + L E + + + L+++L +E EV P
Sbjct: 882 LEEEKEELEEELR---ELESELAELKEEIEK-LRERLEELEAKLERLEVELPE------- 930
Query: 286 IRHEQAGPNVDAVENAEMDEEKRLLQ------GGVDDDDEEEFDDMKERDDILLERLNAI 339
E+ + E++ E L+ G V+ EE+++++ER + L + +
Sbjct: 931 -LEEELEEEYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDL 989
Query: 340 D---KKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNAL 375
+ +KL E + ELD +K + +E + E + +
Sbjct: 990 EEAKEKLLEVIEELD---KEKRERFKETFDKINENFSEI 1025
>gnl|CDD|223662 COG0589, UspA, Universal stress protein UspA and related
nucleotide-binding proteins [Signal transduction
mechanisms].
Length = 154
Score = 37.2 bits (86), Expect = 0.004
Identities = 17/71 (23%), Positives = 25/71 (35%)
Query: 304 DEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEE 363
D + V D +E ++ E L E + T +G E
Sbjct: 44 DPLEPTALVSVALADAPIPLSEEELEEEAEELLAEAKALAEAAGVPVVETEVVEGSPSAE 103
Query: 364 EIRDLAEERNA 374
EI +LAEE +A
Sbjct: 104 EILELAEEEDA 114
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated.
Length = 143
Score = 35.0 bits (81), Expect = 0.023
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 391 KLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQK 439
++I + R KV KGG+ + + A++ GN +G VG K V A++K
Sbjct: 27 RVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKK 75
>gnl|CDD|179208 PRK01026, PRK01026, tetrahydromethanopterin S-methyltransferase
subunit G; Provisional.
Length = 77
Score = 33.0 bits (76), Expect = 0.042
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 303 MDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKK 357
M E++++ Q VD D +E + +RL+ I++K+E AE+ GKK
Sbjct: 1 MAEDEKIPQVVVDPKDFKE----------IQKRLDEIEEKVEFTNAEIFQRIGKK 45
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 35.5 bits (83), Expect = 0.050
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 13/95 (13%)
Query: 291 AGPNVDAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAEL 350
PN + E + DDDE+E ++ E DD L + + +K+ EK L
Sbjct: 174 VDPNAEEDPAHVGSELEE------LDDDEDEEEEEDENDDSLAADESELPEKVLEKFKAL 227
Query: 351 DHTFGKKGKLLEEEI-------RDLAEERNALTEK 378
+ K K E+++ + A+ R L E+
Sbjct: 228 AKQYKKLRKAQEKKVEGRLAQHKKYAKLREKLKEE 262
>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 = 34.7 bits (80), Expect = 0.12
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 15/66 (22%)
Query: 315 DDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNA 374
D +EF D++E L + +++ LE LE+EI +L E N
Sbjct: 62 DVPPSKEFLDLEEEILDLEAEIKEVEENLES---------------LEKEINELEEWLNV 106
Query: 375 LTEKKR 380
L E+K
Sbjct: 107 LDEEKS 112
>gnl|CDD|226550 COG4064, MtrG, Tetrahydromethanopterin S-methyltransferase, subunit
G [Coenzyme metabolism].
Length = 75
Score = 31.2 bits (71), Expect = 0.16
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 10/55 (18%)
Query: 303 MDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKK 357
M EE+++ + VD DD E + +RL+ I++K+E E+ GKK
Sbjct: 1 MSEEEKVPKVVVDPDDFNE----------IHKRLDEIEEKVEFVNGEVYQRIGKK 45
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 34.0 bits (78), Expect = 0.19
Identities = 55/274 (20%), Positives = 111/274 (40%), Gaps = 19/274 (6%)
Query: 116 EKGREREARKRQGLDTK--DIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNLYEEPTDSD 173
EK E + K +++ + E + L+E LE+E E +
Sbjct: 170 EKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEEL-----KELKKLEEIQEE 224
Query: 174 SDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKFEQKHFPL 233
+E++ +A+ +R +++ +R +EL E E+ + + + E++ L
Sbjct: 225 QEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLE-----LEALKIREEELREL 279
Query: 234 RHEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGVIRHEQAGP 293
+ E + RL+E E ++ L+++L L+E E + + +
Sbjct: 280 ERLLEELEEKIERLEELE-REIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKL 338
Query: 294 NVDAVENAEMDEEKRLLQGGVD------DDDEEEFDDMKERDDILLERLNAIDKKLEEKL 347
E E+ EEK L ++ ++ EE + E+ L++L ++L+E+L
Sbjct: 339 EKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEEL 398
Query: 348 AELDHTFGKKGKLLEEEIRDLAEERNALTEKKRR 381
AEL + + LEE ++L E L E +
Sbjct: 399 AELSAALEEIQEELEELEKELEELERELEELEEE 432
Score = 33.2 bits (76), Expect = 0.36
Identities = 57/293 (19%), Positives = 116/293 (39%), Gaps = 29/293 (9%)
Query: 110 LAEVEREKGREREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNLYEEP 169
L E+ERE E + +++++ E + +EKLE++ K +L E
Sbjct: 293 LEELEREIEELEEELEGLRALLEELEEL-LEKLKSLEERLEKLEEKLEKLESELEELAEE 351
Query: 170 TDSDSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKFEQK 229
+ + +ER + +R + +K+ ++ E L+ EA + ++ +
Sbjct: 352 KNELAKLLEERLK--ELEERLEELEKELEKALERLKQLEEAIQ-----ELKEELAELSAA 404
Query: 230 HFPLRHEY----RVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNN------ 279
++ E + + EL L+E E + K + +Q + + E+
Sbjct: 405 LEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCG 464
Query: 280 ---PTNYGVIRHEQAGPNVDAV-ENAEMDEEKRLLQGGVDDDD------EEEFDDMKERD 329
P + E ++ + E ++E+ L+ +++ + EEE ++ E +
Sbjct: 465 QELPEEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELE 524
Query: 330 DILLERLNAIDKKLEEKLAELDHTFGKKGKL-LEEEIRDLAEERNALTEKKRR 381
+ L E L +KLE L EL+ K L+EE+R L + L E
Sbjct: 525 EALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEE 577
>gnl|CDD|234635 PRK00104, scpA, segregation and condensation protein A; Reviewed.
Length = 242
Score = 33.2 bits (77), Expect = 0.20
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 307 KRLLQGGVDDDDEEEFDDMKERDDILLERL------NAIDKKLEEKLAELDHTFGKKGKL 360
K LL + ++EEE D +E LLE+L ++L+E+ E F K
Sbjct: 71 KMLLPKVEEFEEEEE-DPRQE----LLEKLIEYKKFKEAAEELKEQEEERAQYFSKPPSD 125
Query: 361 LEEEIRDLAEER 372
LEE +L E+
Sbjct: 126 LEEFDAELDEDE 137
>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 = 33.1 bits (76), Expect = 0.35
Identities = 34/186 (18%), Positives = 67/186 (36%), Gaps = 31/186 (16%)
Query: 177 DDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKFEQKHFPLRHE 236
++ + + + + +E L A E + ++ + E K LR E
Sbjct: 862 EELEELIEELESELEALLNERASLEEAL-----ALLRSELEELSEELRELESKRSELRRE 916
Query: 237 YRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGVIRHEQAGPNVD 296
+ E + +L+ + + R E+ + A +
Sbjct: 917 LEELREKLAQLELRLEGLEVRIDNLQERLS--EEYSLTLEE-------------AEALEN 961
Query: 297 AVENAEMDEEKRLLQ--------GGVDDDDEEEFDDMKERDDILL---ERLNAIDKKLEE 345
+E+ E + +RL + G V+ EE++++KER D L E L + LEE
Sbjct: 962 KIEDDEEEARRRLKRLENKIKELGPVNLAAIEEYEELKERYDFLTAQKEDLTEAKETLEE 1021
Query: 346 KLAELD 351
+ E+D
Sbjct: 1022 AIEEID 1027
Score = 29.3 bits (66), Expect = 5.4
Identities = 38/245 (15%), Positives = 88/245 (35%), Gaps = 57/245 (23%)
Query: 107 QDLLAEVEREKGREREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNLY 166
L E+ R + +++ R+R + +++ + + +E+LE + + +L
Sbjct: 291 YALANEISRLEQQKQILRERLANLERQLEELEAQ--------LEELESKLDELAEELAEL 342
Query: 167 EEPTDSDSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKF 226
EE + + + + + + + + L+ E +++
Sbjct: 343 EEKLEE-------------LKEELESLEAELEELEAELEELESRLEELEE-----QLETL 384
Query: 227 EQKHFPLRHEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGVI 286
K L + I L N ++ E L+ + R
Sbjct: 385 RSKVAQLELQ---IASLNNEIERLE-ARLERLEDRRER---------------------- 418
Query: 287 RHEQAGPNVDAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEK 346
++ + +E AE+ E + L ++ EEE ++++E + L E L + ++LEE
Sbjct: 419 LQQEIEELLKKLEEAELKELQAEL-----EELEEELEELQEELERLEEALEELREELEEA 473
Query: 347 LAELD 351
LD
Sbjct: 474 EQALD 478
Score = 28.9 bits (65), Expect = 6.3
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 296 DAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFG 355
+ E E + D+ EE +++E+ + L E L +++ +LEE AEL+
Sbjct: 313 NLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEE-LE 371
Query: 356 KKGKLLEEEIRDLAEERNALTEK 378
+ + LEE++ L + L +
Sbjct: 372 SRLEELEEQLETLRSKVAQLELQ 394
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 32.6 bits (75), Expect = 0.41
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 12/72 (16%)
Query: 331 ILLERLNAIDKK-LEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPL------ 383
L E + K LEE + +++ K +E+EI++L EE + L + +
Sbjct: 71 PLREEKKKVSVKSLEELIKDVEEELEK----IEKEIKELEEEISELENEIKELEQEIERL 126
Query: 384 -YRKGFDVKLID 394
FD+ L
Sbjct: 127 EPWGNFDLDLSL 138
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 32.4 bits (74), Expect = 0.49
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 305 EEKRLLQGGVDDDDE-EEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEE 363
EE+RL+Q D E+ D+++ + + + L+A + +LEE +LD+ + L E
Sbjct: 82 EEERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPE 141
Query: 364 EIRDL 368
+ R L
Sbjct: 142 QARKL 146
Score = 30.1 bits (68), Expect = 2.5
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 1/86 (1%)
Query: 301 AEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKL 360
E + L + +E +E ERL +++L+ + +LD+ + +
Sbjct: 51 EAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEEQLDARAEKLDNLENQLEE- 109
Query: 361 LEEEIRDLAEERNALTEKKRRPLYRK 386
E+ + E L ++ LYR
Sbjct: 110 REKALSARELELEELEKQLDNELYRV 135
>gnl|CDD|163705 cd00328, catalase, Catalase heme-binding enzyme. Catalase is a
ubiquitous enzyme found in both prokaryotes and
eukaryotes, which is involved in the protection of cells
from the toxic effects of peroxides. It catalyzes the
conversion of hydrogen peroxide to water and molecular
oxygen. Catalases also utilize hydrogen peroxide to
oxidize various substrates such as alcohol or phenols.
Most catalases exist as tetramers of 65KD subunits
containing a protoheme IX group buried deep inside the
structure. In eukaryotic cells, catalases are located in
peroxisomes.
Length = 433
Score = 32.0 bits (73), Expect = 0.55
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 25 TPLSFSRKISTFPHFLTNQTPPNPLPPRTHFPNASQEYSA 64
TP+ F R FP F+ Q P P+T P+A + +
Sbjct: 83 TPIFFIRDAIKFPDFIHAQKP----NPQTALPDADRFWDF 118
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.8 bits (73), Expect = 0.60
Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 19/94 (20%)
Query: 325 MKERDDI-------LLERLNAIDKKLEEKLAELDHTFGKKG-----------KLLEEEIR 366
+KE + L R + KK+ E +AE+D K G EE ++
Sbjct: 10 LKEYEKRRDKEELELKNRKEEVYKKIPE-IAEIDDEIAKLGIKLSRAILKNPDKKEETLK 68
Query: 367 DLAEERNALTEKKRRPLYRKGFDVKLIDVNRTCK 400
+L E+ L KK L G+ +++ TC
Sbjct: 69 ELKEKITDLRVKKAELLVSNGYPPDYLEMKYTCP 102
>gnl|CDD|217956 pfam04194, PDCD2_C, Programmed cell death protein 2, C-terminal
putative domain.
Length = 165
Score = 30.8 bits (70), Expect = 0.88
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 135 DQEDEEDYMGVGPLIEKLEKERLKDTGDLNLYEEPTDSDSDEDDERFSRDAVNKRFQVFQ 194
+E+E + + L E+ E+ + +L D +E DE + +K FQ F+
Sbjct: 8 PEEEEYETLHAPSLPEEPEEREIDAFEELEKEGGGGKED-EETDESEKAKSDDKTFQKFK 66
Query: 195 K 195
K
Sbjct: 67 K 67
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 31.8 bits (73), Expect = 0.91
Identities = 28/112 (25%), Positives = 47/112 (41%), Gaps = 16/112 (14%)
Query: 291 AGPNVDAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDIL--LER---LNAIDKKLEE 345
G +E +DEE + D++KE I ER L+AI +K+EE
Sbjct: 225 VGKKKWELEPPSLDEE------LEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEE 278
Query: 346 KLAELDHTFGKKGKLLEEEIRDL--AEERNALTEKKRRPLYRKGFDVKLIDV 395
+L+ + + K ++ + L R + E K R R G +V+ I +
Sbjct: 279 ELSGEEES---SLKEIKAILEKLEKKPVRRLILEGKVRIDGRFGDEVRPIGI 327
>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 = 30.5 bits (69), Expect = 1.1
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 19/93 (20%)
Query: 298 VENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAID----------KKLEEKL 347
E+ E K+ L + +EE +D++ER L L + K LEE+L
Sbjct: 76 ELQGELSELKQQLS-----ELQEELEDLEERIAELESELEDLKEDLQLLRELLKSLEERL 130
Query: 348 AELDHTFGKKGKLLEEEIRDLAEERNALTEKKR 380
L+ + K L +E+R+L ++ E+ R
Sbjct: 131 ESLEESI----KELAKELRELRQDLREEVEELR 159
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 30.8 bits (70), Expect = 1.6
Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 4/97 (4%)
Query: 315 DDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNA 374
+D+ E ++ K D L E ++ +D +++ LD K E EE A
Sbjct: 20 EDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASGEGG-GGEEEEEEA 78
Query: 375 LTEKKRRPLYRKGFDVKLIDVNRTCKVT---KGGQVV 408
E Y +G D L + + GG +V
Sbjct: 79 KAEAAEFRAYLRGGDDALAEERKALSTGTDSDGGYLV 115
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 30.2 bits (69), Expect = 1.7
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 7/89 (7%)
Query: 293 PNVDAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKL-EEKLAELD 351
PN A E L + ++DDD+++ D+ +D E D + E+ AEL
Sbjct: 32 PNAAAAAATAAAIESELDEEDLEDDDDDDEDE---DEDDEEEADLGPDPEEARERFAELR 88
Query: 352 HTFGKKGKLLEEEIRDLA---EERNALTE 377
+ K K +E+ R + R AL E
Sbjct: 89 EQYEKTRKAIEKHGRGSKKAQKAREALAE 117
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 30.7 bits (70), Expect = 1.7
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 295 VDAVENAEMD----EEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAEL 350
+D E+D EE+ + DDDDE++ DM + D+ + ++E +L
Sbjct: 214 LDVEIQNELDDIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPEVERTSTIKEVSEKL 273
Query: 351 D 351
D
Sbjct: 274 D 274
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 30.5 bits (69), Expect = 1.7
Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 7/60 (11%)
Query: 18 NLKNPTKTPLSFSRKISTFP--HFLTNQTPPNPLPPRTHFPNASQEYSAKPIYSFSRKIS 75
NLKNP SF R P ++ + P L F + + IY SRK S
Sbjct: 185 NLKNPQIFCTSFDR-----PNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKS 239
>gnl|CDD|112777 pfam03978, Borrelia_REV, Borrelia burgdorferi REV protein. This
family consists of several REV proteins from Borrelia
burgdorferi (Lyme disease spirochete). The function of
REV is unknown although it known that gene is induced
during the ingesting of host blood suggesting a role in
the metabolic activation of borreliae to adapt to
physiological stimuli.
Length = 160
Score = 29.8 bits (67), Expect = 1.8
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 314 VDDDDEEEFDDMKERDDILLERL-NAIDKKLEEKLAELDHTFGKK 357
+ DE +F + KE+ + L E L + + +LEEKL L F K
Sbjct: 41 NNKSDETKFKNYKEKINELKEDLKDVGNAELEEKLLNLQSLFQDK 85
>gnl|CDD|188547 TIGR04032, toxin_SdpC, antimicrobial peptide, SdpC family. This
protein family contains the antimicrobial peptide SdpC,
used in cannibalistic killing by Bacillus subtilis, and
related sequences in species as distant as Myxococcus
xanthus from the Deltaproteobacteria. A conserved gene
neighborhood includes proteins associated with immunity.
Length = 172
Score = 29.7 bits (67), Expect = 2.0
Identities = 14/89 (15%), Positives = 25/89 (28%), Gaps = 21/89 (23%)
Query: 144 GVGPLIEKLEKERLKDTGDLNLYEEPTDSDSDED----------------DERFSRDAVN 187
G GP +KL + NL + +S ++ +R +
Sbjct: 19 GQGPAAKKLPEL-----WQKNLIKAYNNSPEAKELANDLIAKIKKKDPAYFDRLKEAVYS 73
Query: 188 KRFQVFQKKFKRHKELLQNFTEAETPDEA 216
+ + ELLQ T +
Sbjct: 74 GDPLKVDELLTKGGELLQEAAAESTAALS 102
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 30.6 bits (69), Expect = 2.0
Identities = 22/108 (20%), Positives = 39/108 (36%), Gaps = 22/108 (20%)
Query: 296 DAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFG 355
+AVE A DE L + EE D++K + +L + E + E+ +
Sbjct: 266 EAVEGAVKDELSAALTIAGKQEREEALDEVKAL---VAAKLAE---QFEGREKEISAAYR 319
Query: 356 K------KGKLLEE----------EIRDLAEERNALTEKKRRPLYRKG 387
+ ++L E +IR L E + L+ +G
Sbjct: 320 AVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERG 367
>gnl|CDD|130859 TIGR01800, cit_synth_II, 2-methylcitrate synthase/citrate synthase
II. Members of this family are dimeric enzymes with
activity as 2-methylcitrate synthase, citrate synthase,
or both. Many Gram-negative species have a hexameric
citrate synthase, termed citrate synthase I (TIGR01798).
Members of this family (TIGR01800) appear as a second
citrate synthase isozyme but typically are associated
with propionate metabolism and synthesize
2-methylcitrate from propionyl-CoA; citrate synthase
activity may be incidental. A number of species,
including Thermoplasma acidophilum, Pyrococcus furiosus,
and the Antarctic bacterium DS2-3R have a bifunctional
member of this family as the only citrate synthase
isozyme.
Length = 368
Score = 30.0 bits (68), Expect = 2.2
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 207 FTEAETPDEAFKWMNK-IDKFEQ---------KHFPLRHEYRVIGELMNRLKEAEGKDK- 255
E PD+A W+ K ++ E+ K + R +++ E +L EG K
Sbjct: 226 LDEIGDPDKAEAWIRKALENKERIMGFGHRVYKTYDPRA--KILKEYAKKLSAKEGSSKW 283
Query: 256 FMLQQKLNRAMRLVEWKEVYDPN 278
+ + ++L M E K +Y PN
Sbjct: 284 YEIAERLEDVM--EEEKGIY-PN 303
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 30.4 bits (68), Expect = 2.3
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 160 TGDLNLYEEPTDSDSDEDDERFSRDAVNKRFQV 192
T DLN Y +P ++ +ED S DAV +R ++
Sbjct: 1178 TLDLNYYHDPHSTEIEEDGSTISDDAVKQRGEI 1210
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 30.4 bits (69), Expect = 2.5
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 301 AEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKL 360
AE E KR L+ D+ EE + KER + LE+ +++KL+E E D + G +
Sbjct: 630 AEKRERKRELEAEFDEARIEEAREDKERAEEYLEQ---VEEKLDELREERDDLQAEIGAV 686
Query: 361 LEE--EIRDLAEERNALTEKKRR 381
E E+ +L E R AL +
Sbjct: 687 ENELEELEELRERREALENRVEA 709
>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 = 30.0 bits (68), Expect = 3.0
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 319 EEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEK 378
EE+ ++KE + L L +DK+ E EL K E++ L E N L +
Sbjct: 356 TEEYAELKEELEDLRAELEEVDKEFAETRDEL--------KDYREKLEKLKREINELKRE 407
Query: 379 KRRPLYRK 386
R
Sbjct: 408 LDRLQEEL 415
Score = 28.9 bits (65), Expect = 6.7
Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 297 AVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGK 356
+E A D E RL + + E +E I RL I++KL E
Sbjct: 776 KLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIE-ARLREIEQKLNRLTLEK------ 828
Query: 357 KGKLLEEEIRDLAEERNALTEKK 379
+ LE+EI++L E+R L E+
Sbjct: 829 --EYLEKEIQELQEQRIDLKEQI 849
>gnl|CDD|239896 cd04449, DEP_DEPDC5-like, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in DEPDC5-like proteins. DEPDC5, in human
also known as KIAA0645, is a DEP domain containing
protein of unknown function.
Length = 83
Score = 27.6 bits (62), Expect = 3.5
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 203 LLQNFTEAETPDEAFKWMNK 222
L+ NF + +T +EA + +
Sbjct: 39 LINNFEDVDTREEAVELGQE 58
>gnl|CDD|197369 cd09909, HIV-1-like_HR1-HR2, heptad repeat 1-heptad repeat 2 region
(ectodomain) of the gp41 subunit of human
immunodeficiency virus (HIV-1), and related domains.
This domain family spans both heptad repeats of the
glycoprotein (gp)/transmembrane subunit of various
endogenous retroviruses (ERVs) and infectious
retroviruses, including human, simian, and feline
immunodeficiency viruses (HIV, SIV, and FIV), bovine
immunodeficiency-like virus (BIV), equine infectious
anaemia virus (EIAV), and Jaagsiekte sheep retrovirus
(JSRV), mouse mammary tumour virus (MMTV) and various
ERVs including sheep enJSRV-26, and human ERVs (HERVs):
HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs
to a larger superfamily containing the HR1-HR2 domain of
ERVs and infectious retroviruses, including Ebola virus,
and Rous sarcoma virus. Proteins in this family lack the
canonical CSK17-like immunosuppressive sequence, and the
intrasubunit disulfide bond-forming CX6C motif found in
linker region between HR1 and HR2 in the
Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2
region is a fusion peptide (FP), and C-terminal is a
membrane-spanning region (MSR). Viral infection involves
the formation of a trimer-of-hairpins structure (three
HR1 helices, buttressed by three HR2 helices lying in
antiparallel orientation). In this structure, the FP
(inserted in the host cell membrane) and MSR (inserted
in the viral membrane) are in close proximity. ERVs are
likely to originate from ancient germ-line infections by
active retroviruses. Some modern ERVs, those that
integrated into the host genome post-speciation, have a
currently active exogenous counterpart, such as JSRV.
Some ERVs play specific roles in the host, including
placental development, protection of the host from
infection by related pathogenic and exogenous
retroviruses, and genome plasticity. Included in this
subgroup are ERVs from domestic sheep that are related
to JSRV, the agent of transmissible lung cancer in
sheep, for example enJSRV-26 that retains an intact
genome. These endogenous JSRVs protect the sheep against
JSRV infection and are required for sheep placental
development. HERV-K_c12q14.1 is potentially a complete
envelope protein; however, it does not appear to be
fusogenic.
Length = 128
Score = 28.5 bits (64), Expect = 3.7
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 218 KWMNKIDKFEQKHFPLRHE 236
+W NKID E+K L E
Sbjct: 93 EWENKIDDLEEKILNLLEE 111
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.7 bits (68), Expect = 3.7
Identities = 22/86 (25%), Positives = 47/86 (54%), Gaps = 8/86 (9%)
Query: 296 DAVENAEMDEEKRLLQGGVDDDDEEEFDDMKER-DDILLERLNAIDKKLEEKLAELDHTF 354
+A + AE +++ LL+ +EE ++ + L ER N + +KLE++L + +
Sbjct: 46 EAKKEAEAIKKEALLEA------KEEIHKLRNEFEKELRERRNEL-QKLEKRLLQKEENL 98
Query: 355 GKKGKLLEEEIRDLAEERNALTEKKR 380
+K +LLE+ +L ++ L +K++
Sbjct: 99 DRKLELLEKREEELEKKEKELEQKQQ 124
>gnl|CDD|188151 TIGR01517, ATPase-IIB_Ca, plasma-membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
plasma membrane of eukaryotes , out of the cell. In some
organisms, this type of pump may also be found in
vacuolar membranes. In humans and mice, at least, there
are multiple isoforms of the PMCA pump with overlapping
but not redundant functions. Accordingly, there are no
human diseases linked to PMCA defects, although
alterations of PMCA function do elicit physiological
effects. The calcium P-type ATPases have been
characterized as Type IIB based on a phylogenetic
analysis which distinguishes this group from the Type
IIA SERCA calcium pump. A separate analysis divides Type
IIA into sub-types (SERCA and PMR1) which are modelled
by TIGR01116 and TIGR01522. This model is well separated
from those.
Length = 944
Score = 29.7 bits (67), Expect = 3.8
Identities = 14/65 (21%), Positives = 22/65 (33%), Gaps = 7/65 (10%)
Query: 323 DDMKERDDILLE--RLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKR 380
D K + + I KL+ L E G + E R+ +N L EK
Sbjct: 30 DIFKRAMPLYEKLGGAEGIATKLKTDLNE-----GVRLSSSTLERREKVYGKNELPEKPP 84
Query: 381 RPLYR 385
+ +
Sbjct: 85 KSFLQ 89
>gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter;
Provisional.
Length = 490
Score = 29.7 bits (67), Expect = 3.9
Identities = 12/55 (21%), Positives = 29/55 (52%), Gaps = 15/55 (27%)
Query: 324 DMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEK 378
D++E +IL+E + I++K+++ +++EI +L +R L ++
Sbjct: 446 DIQEAKEILVEHYDNIEQKIDD---------------IDQEIAELQAKRTRLVQQ 485
>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 = 28.8 bits (65), Expect = 4.1
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 338 AIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYRK 386
A K+LE++ +L KK K L++E + L ++ L+E+ R+ ++
Sbjct: 35 AAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQE 83
>gnl|CDD|215079 PLN00151, PLN00151, potassium transporter; Provisional.
Length = 852
Score = 29.7 bits (67), Expect = 4.3
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 132 KDIDQEDEEDYMGVGPLIEKLEKERLKDTGDLNLYEEPTDSDSDEDDERFSRD 184
KD+ +E+ + + + LIE LEK ++ + L E + D+D++D S
Sbjct: 678 KDVRKENHQAFEQL--LIESLEKFIRREAQERAL-ESDGNDDTDDEDSVTSSR 727
>gnl|CDD|235580 PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase
subunit alpha; Validated.
Length = 319
Score = 29.0 bits (66), Expect = 4.6
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 341 KKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEK 378
+LE K+ EL L EEI L ++ LT+K
Sbjct: 13 AELEAKIEELRAVAEDSDVDLSEEIERLEKKLEELTKK 50
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 28.9 bits (65), Expect = 4.7
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 318 DEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTE 377
DE E + I ER+N+ LE++LAEL K K +E+ L L E
Sbjct: 87 DERELRALNIEIQIAKERINS----LEDELAELMEEIEKLEKEIEDLKERLERLEKNLAE 142
Query: 378 KKRR 381
+ R
Sbjct: 143 AEAR 146
>gnl|CDD|201397 pfam00690, Cation_ATPase_N, Cation transporter/ATPase, N-terminus.
Members of this families are involved in Na+/K+, H+/K+,
Ca++ and Mg++ transport.
Length = 69
Score = 26.7 bits (60), Expect = 4.8
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 343 LEEKLAELDHTFGKKGKLLEEEIRDLAEE--RNALTEKKRRPLYRK 386
+EE LA L +KG L E E + E+ N L EKK + L++
Sbjct: 6 VEEVLARLGTDL-EKG-LTEAEAEERLEKYGPNELPEKKPKSLWKI 49
>gnl|CDD|177781 PLN00187, PLN00187, photosystem II light-harvesting complex II
protein Lhcb4; Provisional.
Length = 286
Score = 29.0 bits (65), Expect = 5.0
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 14/53 (26%)
Query: 300 NAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDH 352
NAE+D EKRL GG + FD + D +KK +LAE+ H
Sbjct: 204 NAELDPEKRLYPGG------KFFDPLGLAAD--------PEKKETLQLAEIKH 242
>gnl|CDD|113000 pfam04210, MtrG, Tetrahydromethanopterin S-methyltransferase,
subunit G. The N5-methyltetrahydromethanopterin:
coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is
a membrane-associated, corrinoid-containing protein that
uses a transmethylation reaction to drive an
energy-conserving sodium ion pump.
Length = 70
Score = 26.6 bits (59), Expect = 5.2
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 327 ERDDI--LLERLNAIDKKLEEKLAELDHTFGKK 357
DD + +RL+ I++K+E E+ GKK
Sbjct: 10 PPDDFNEIHKRLDEIEEKVEFVNGEVYQRIGKK 42
>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 = 29.0 bits (65), Expect = 5.5
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 320 EEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKK 379
+ + KE ++L+E+L+A++K+LE+K L+ K+ + L++E+ EE K
Sbjct: 504 TFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLL-KEQEKLKKELEQEMEELKERERNK 562
Query: 380 RRPLYR 385
+ L +
Sbjct: 563 KLELEK 568
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 29.1 bits (66), Expect = 5.5
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 9/50 (18%)
Query: 317 DDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIR 366
+++ E + + E+L + +L+E LA K+GK+L E ++
Sbjct: 179 EEDIEELV----LEKIREKLEELIAELDELLAT-----AKQGKILREGLK 219
>gnl|CDD|130219 TIGR01149, mtrG, N5-methyltetrahydromethanopterin:coenzyme M
methyltransferase subunit G. This model describes
N5-methyltetrahydromethanopterin: coenzyme M
methyltransferase subunit G in methanogenic archaea.
This methyltranfersae is membrane-associated enzyme
complex that uses methyl-transfer reaction to drive
sodium-ion pump. Archaea have evolved energy-yielding
pathways marked by one-carbon biochemistry featuring
novel cofactors and enzymes. This transferase is
involved in the transfer of 'methyl' group from
N5-methyltetrahydromethanopterin to coenzyme M. In an
accompanying reaction, methane is produced by
two-electron reduction of the methyl moiety in
methyl-coenzyme M by another enzyme methyl-coenzyme M
reductase [Energy metabolism, Other].
Length = 70
Score = 26.6 bits (59), Expect = 6.0
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 327 ERDDI--LLERLNAIDKKLEEKLAELDHTFGKK 357
E D+ +++RL+ I++K+E E+ GKK
Sbjct: 10 EPDEFNEVMKRLDEIEEKVEFVNGEVAQRIGKK 42
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 29.1 bits (66), Expect = 6.1
Identities = 38/266 (14%), Positives = 98/266 (36%), Gaps = 59/266 (22%)
Query: 173 DSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKW-MNKIDKFEQKHF 231
D+ E +++A + +Q +++ + ++L + E + ++ + ++++
Sbjct: 146 DAFAGLEELAQEAYQEAYQAWKQARRELEDLQEKERERAQRADLLQFQLEELEELN---- 201
Query: 232 PLRHEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGVIRH--- 288
E + E RL +E L + + A+ L+ + + + ++
Sbjct: 202 LQPGEDEELEEERKRLSNSE-----KLAEAIQNALELLS----GEDDTVSALSLLGRALE 252
Query: 289 ---------EQAGPNVDAVENA--EMDEEKRLLQGGVD--DDDEEEFDDMKER------- 328
+ + +E A E++E L+ +D + D ++++ER
Sbjct: 253 ALEDLSEYDGKLSELAELLEEALYELEEASEELRAYLDELEFDPNRLEEVEERLFALKSL 312
Query: 329 --------DDIL------LERLNAID------KKLEEKLAELDHTFGKKGKLLEEEIRDL 368
+D+L E L +D + LE+++ +L + + L +
Sbjct: 313 ARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSAIRKKA 372
Query: 369 AEERNALTEKKRRPLYRKG--FDVKL 392
A+E + + L + F V+L
Sbjct: 373 AKELEKEVTAELKALAMEKARFTVEL 398
>gnl|CDD|189013 cd09606, M3B_PepF_1, 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 = 546
Score = 28.7 bits (65), Expect = 6.5
Identities = 6/35 (17%), Positives = 16/35 (45%)
Query: 193 FQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKFE 227
F+ +R +L+ A++ +E W+ + +
Sbjct: 6 FEALKERFIDLIAKLKNAKSAEELEAWLKEWSELR 40
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 28.4 bits (64), Expect = 7.1
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 325 MKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDL 368
ER+ +L E+ ++ KL+E+ L F + + L++EI+DL
Sbjct: 253 EAEREKLLAEQERMLEHKLQEQEELLKEGFKTEAESLQKEIQDL 296
>gnl|CDD|220888 pfam10846, DUF2722, Protein of unknown function (DUF2722). This
eukaryotic family of proteins has no known function.
Length = 373
Score = 28.3 bits (63), Expect = 8.0
Identities = 14/64 (21%), Positives = 20/64 (31%), Gaps = 2/64 (3%)
Query: 16 NQNLKNPTKTPLSFSRKISTFP-HFLTNQTPPNPLPPRTHFPNASQEYSAKPIYSFSRKI 74
N N+ P + L+F P H + P T F + Q R
Sbjct: 232 NSNIPKPATSVLNFK-PSPAQPLHKQSKSAPQPSQESMTSFQHIIQWKPESQQKKHRRTK 290
Query: 75 STFS 78
S+ S
Sbjct: 291 SSSS 294
>gnl|CDD|224273 COG1354, scpA, Rec8/ScpA/Scc1-like protein (kleisin family)
[Replication, recombination, and repair].
Length = 248
Score = 28.0 bits (63), Expect = 8.0
Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 12/91 (13%)
Query: 307 KRLLQGGVDDDDEEEFDDMKE---RDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEE 363
+ LL ++ ++EE ++ ++ ER + L E E F K K +
Sbjct: 72 RMLLPKEEEEAEDEELEEPRDELVARLEEYERYKEAAELLAELEEERRDVF-SKIKPEIK 130
Query: 364 EIR--------DLAEERNALTEKKRRPLYRK 386
+ L + A + RR +
Sbjct: 131 IKKERRPVEEISLIDLFRAYQKILRRVKQEE 161
>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional.
Length = 177
Score = 27.9 bits (62), Expect = 8.4
Identities = 13/57 (22%), Positives = 28/57 (49%)
Query: 150 EKLEKERLKDTGDLNLYEEPTDSDSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQN 206
E+++ E +++ + EE + +E E+ + N+R F+ K+ R +QN
Sbjct: 3 EEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFENKYLRAHAEMQN 59
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 28.6 bits (65), Expect = 9.0
Identities = 29/124 (23%), Positives = 49/124 (39%), Gaps = 46/124 (37%)
Query: 294 NVDAVENA--EMDEEK-----RLLQG--------------GVDD-----------DDEEE 321
N + VENA E DEE RLL G G+ + +D+E+
Sbjct: 458 NREGVENASVEFDEETLRPTYRLLIGIPGKSNAFEIAKRLGLPENIIEEAKKLIGEDKEK 517
Query: 322 FDDM------KERD--------DILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRD 367
+++ ER+ + LL+ + ++LEEK +L K + E+E +
Sbjct: 518 LNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQ 577
Query: 368 LAEE 371
+E
Sbjct: 578 AIKE 581
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.2 bits (64), Expect = 9.4
Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 9/50 (18%)
Query: 317 DDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIR 366
+++ EF D+ +LE+L + +LE LA ++G++L E ++
Sbjct: 177 EEDIEFLS----DEKILEKLEELIAELEALLAS-----ARQGEILREGLK 217
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 28.4 bits (64), Expect = 9.8
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 2/82 (2%)
Query: 296 DAVENAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFG 355
A ++ + D++ L +DDDD++E DD + DD + + + E + D
Sbjct: 129 QADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDD--DD 186
Query: 356 KKGKLLEEEIRDLAEERNALTE 377
+ E A + LT
Sbjct: 187 FVWDEDDSEALRQARKDAKLTA 208
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 28.5 bits (65), Expect = 10.0
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 338 AIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEE 371
+D+ E L EL ++ LE+EI +LA E
Sbjct: 499 KVDR---EYLKELSAELAQRLAELEQEIYELAGE 529
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
0.314 0.133 0.383
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: 23,617,809
Number of extensions: 2436456
Number of successful extensions: 3380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3208
Number of HSP's successfully gapped: 264
Length of query: 442
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 342
Effective length of database: 6,502,202
Effective search space: 2223753084
Effective search space used: 2223753084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 61 (27.2 bits)