RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2640
(613 letters)
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 269 bits (691), Expect = 1e-85
Identities = 110/290 (37%), Positives = 146/290 (50%), Gaps = 75/290 (25%)
Query: 84 ISVYVCGNTSTTSGLTVTLSR-EGGGDFALEAGALVLADQGVCCIDEFDKMSAQHQNGML 142
+VY G S+ +GLT + R G++ LEAGALVLAD GVCCIDEFDKM+ + +
Sbjct: 83 RAVYTSGKGSSAAGLTAAVVRDPDTGEWTLEAGALVLADGGVCCIDEFDKMNEEDRV--- 139
Query: 143 YTAKAMRGITSRQYTPAFITMSIHPVMGEKRHTMSAQHQALLEAMEQQSISIAKASVVCS 202
A+ EAMEQQ+ISIAKA +V +
Sbjct: 140 ---------------------------------------AIHEAMEQQTISIAKAGIVAT 160
Query: 203 LPARTSVIAAANPVGGHYNRAKTVAENLRMGQALLSRFDLVFILLDNPDEHLDTLLSEHV 262
L AR SV+AAANP+ G Y+ K+VAEN+ + LLSRFDL+F+LLD PDE D L++H+
Sbjct: 161 LNARCSVLAAANPIFGRYDPKKSVAENINLPPPLLSRFDLIFVLLDKPDEERDEELAKHI 220
Query: 263 MASLSGFQSNRNPSHSTQSFTENPNSVQSDIPLSERLKPGPGEELPLIPAPLLHKYLAYA 322
+ E I LL KY+AYA
Sbjct: 221 VDLHRASDEEE------------------------------IETEDEIDPELLRKYIAYA 250
Query: 323 RKYVSKPELSTEAALLLQEFYLNLRK-HHHSVDATPVTTRQLESLVRLTQ 371
R+ + KP+LS EA L +Y+ LRK S + P+T RQLESL+RL++
Sbjct: 251 RENI-KPKLSDEAREKLVNWYVELRKESEGSRGSIPITVRQLESLIRLSE 299
Score = 99.5 bits (249), Expect = 6e-23
Identities = 34/95 (35%), Positives = 51/95 (53%), Gaps = 17/95 (17%)
Query: 371 QDIQAEPNLFKLLVNSLCPSIFGHEMVKAGLLLALFGGCHSTNGS----RGDAHVLIVGD 426
+++ +P+++ L S+ PSI+GHE VK +LL LFGG RGD +VL+VGD
Sbjct: 6 RELAKDPDIYDKLARSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRLRGDINVLLVGD 65
Query: 427 PGLGKSQMLHACCAAKKFISVLQKKAEVQSRSVFT 461
PG KSQ+L ++ R+V+T
Sbjct: 66 PGTAKSQLLKYVA-------------KLAPRAVYT 87
Score = 37.5 bits (88), Expect = 0.015
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 565 QLMS------ARAKCELREEASKQDAQDVIDIMKWSLI 596
QL S A A+ L EE +++D ++ I ++ SL
Sbjct: 290 QLESLIRLSEAHARLRLSEEVTEEDVEEAIRLILESLK 327
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 241 bits (616), Expect = 8e-71
Identities = 108/305 (35%), Positives = 151/305 (49%), Gaps = 76/305 (24%)
Query: 79 MHHYII-----SVYVCGNTSTTSGLTVTLSR-EGGGDFALEAGALVLADQGVCCIDEFDK 132
+ Y+ VY G S+ +GLT + R + G++ LEAGALVLAD GVCCIDEFDK
Sbjct: 335 LLKYVAKLAPRGVYTSGKGSSAAGLTAAVVRDKVTGEWVLEAGALVLADGGVCCIDEFDK 394
Query: 133 MSAQHQNGMLYTAKAMRGITSRQYTPAFITMSIHPVMGEKRHTMSAQHQALLEAMEQQSI 192
M+ + + A+ EAMEQQ+I
Sbjct: 395 MNEEDRV------------------------------------------AIHEAMEQQTI 412
Query: 193 SIAKASVVCSLPARTSVIAAANPVGGHYNRAKTVAENLRMGQALLSRFDLVFILLDNPDE 252
SIAKA + +L AR SV+AAANP G Y+ KTVAEN+ + LLSRFDL+F+L D+PDE
Sbjct: 413 SIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDLIFVLKDDPDE 472
Query: 253 HLDTLLSEHVMASLSGFQSNRNPSHSTQSFTENPNSVQSDIPLSERLKPGPGEELPLIPA 312
D ++EH++ T + + V +E+
Sbjct: 473 EKDEEIAEHIL---------DKHRGEEPEETISLDGV---------------DEVEERDF 508
Query: 313 PLLHKYLAYARKYVSKPELSTEAALLLQEFYLNLRKHHHSVDAT---PVTTRQLESLVRL 369
LL KY++YARK V P L+ EA L+++Y+ +RK V+ P+T RQLES++RL
Sbjct: 509 ELLRKYISYARKNV-TPVLTEEAREELEDYYVEMRKKSALVEEKRTIPITARQLESIIRL 567
Query: 370 TQDIQ 374
+
Sbjct: 568 AEAHA 572
Score = 94.3 bits (235), Expect = 3e-20
Identities = 36/98 (36%), Positives = 55/98 (56%), Gaps = 11/98 (11%)
Query: 353 VDATPVTTRQLESLVRLTQD-------IQAEPNLFKLLVNSLCPSIFGHEMVKAGLLLAL 405
++A V V +T++ + P+++ +L+ S+ PSI+GHE VK +LL L
Sbjct: 243 LEANSVEKLDKREEVEITEEDEEEIKELAKRPDIYDILIKSIAPSIYGHEDVKKAILLQL 302
Query: 406 FGGCH--STNGS--RGDAHVLIVGDPGLGKSQMLHACC 439
FGG +G+ RGD H+L+VGDPG KSQ+L
Sbjct: 303 FGGVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVA 340
Score = 31.9 bits (73), Expect = 1.2
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 565 QLMSARAKCELREEASKQDAQDVIDIMKWSLIDTSLNGGGGI 606
+L A AK L + ++D + I ++ +SL +++ G
Sbjct: 566 RLAEAHAKMRLSDVVEEEDVDEAIRLVDFSLKTVAVDPEKGK 607
>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 221 bits (566), Expect = 4e-65
Identities = 105/292 (35%), Positives = 143/292 (48%), Gaps = 76/292 (26%)
Query: 84 ISVYVCGNTSTTSGLTVTLSR-EGGGDFALEAGALVLADQGVCCIDEFDKMSAQHQNGML 142
+VY G S+ GLT ++R +F LEAGALVLAD GVCCIDEFDKM +
Sbjct: 262 RAVYTTGKGSSAVGLTAAVTRDPETREFTLEAGALVLADNGVCCIDEFDKMDDSDR---- 317
Query: 143 YTAKAMRGITSRQYTPAFITMSIHPVMGEKRHTMSAQHQALLEAMEQQSISIAKASVVCS 202
+IH EAMEQQ+ISIAKA + +
Sbjct: 318 --------------------TAIH------------------EAMEQQTISIAKAGITTT 339
Query: 203 LPARTSVIAAANPVGGHYNRAKTVAENLRMGQALLSRFDLVFILLDNPDEHLDTLLSEHV 262
L AR SV+AAANP+GG Y+ T EN+ + +LSRFDL+F++LD DE D L++HV
Sbjct: 340 LNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILSRFDLLFVVLDEVDEERDRELAKHV 399
Query: 263 MASLSGFQSNRNPSHSTQSFTENPNSVQSDIPLSERLKPGPGEELPLIPAPLLHKYLAYA 322
+ +P P + L KY+AYA
Sbjct: 400 VDL----HRYSHPEEDEA-------------------------FEPPLSQEKLRKYIAYA 430
Query: 323 RKYVSKPELSTEAALLLQEFYLNLRKHHHSVDAT---PVTTRQLESLVRLTQ 371
R+ + KP+LS EAA L + Y++LRK ++ P+T RQLES++RL++
Sbjct: 431 REKI-KPKLSEEAADKLVKAYVDLRKEDSQTESRSSIPITVRQLESIIRLSE 481
Score = 86.5 bits (215), Expect = 7e-18
Identities = 37/115 (32%), Positives = 61/115 (53%), Gaps = 18/115 (15%)
Query: 352 SVDATPVTTRQLESL-VRLTQDIQAEPNLFKLLVNSLCPSIFGHEMVKAGLLLALFGGCH 410
S + + + + L + + +P++++ L SL PSI+GHE +K +LL LFGG H
Sbjct: 165 SFEDSSFSVQSLSDEEEEEIRKLSKDPDIYERLARSLAPSIYGHEDIKKAILLLLFGGVH 224
Query: 411 --STNGS--RGDAHVLIVGDPGLGKSQMLHACCAAKKFISVLQKKAEVQSRSVFT 461
+G RGD ++L+ GDPG KSQ+L K++ + R+V+T
Sbjct: 225 KNLPDGMKIRGDINILLCGDPGTAKSQLL-------KYVE------KTAPRAVYT 266
>gnl|CDD|173403 PTZ00111, PTZ00111, DNA replication licensing factor MCM4;
Provisional.
Length = 915
Score = 123 bits (310), Expect = 2e-29
Identities = 74/320 (23%), Positives = 143/320 (44%), Gaps = 86/320 (26%)
Query: 85 SVYVCGNTSTTSGLTVTLSREGG--GDFALEAGALVLADQGVCCIDEFDKMSAQHQNGML 142
S+Y G +S++ GLT ++ G ++ GA+VLA+ GVCCIDE DK H L
Sbjct: 519 SIYTSGKSSSSVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKC---HNESRL 575
Query: 143 YTAKAMRGITSRQYTPAFITMSIHPVMGEKRHTMSAQHQALLEAMEQQSISIAKASVVCS 202
+L E MEQQ+++IAKA +V +
Sbjct: 576 ---------------------------------------SLYEVMEQQTVTIAKAGIVAT 596
Query: 203 LPARTSVIAAANPVGGHYNRAKTVAENLRMGQALLSRFDLVFILLDNPDEHLDTLLS--- 259
L A T+++A+ NP+ YN+ K V EN+ + +L +RFDL++++LD+ D+ D L+S
Sbjct: 597 LKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQDTDQLISLSI 656
Query: 260 --EHVMASLSGFQSNRNPSHSTQSFTENPNSVQSDIPLSERLKPGPGEELPLIPAPLLHK 317
+ ++ ++G ++ + + + S++S+ ++ +L
Sbjct: 657 AKDFLLPHMTGSGNDEDTYDRSNTMHVEDESLRSE------------KDYNKNDLDMLRM 704
Query: 318 YLAYARKYVSKPELSTEAALLLQEFYLNLRKHHHSVDATP-------------------- 357
Y+ +++ + P+LS EA ++ Y+ +R+ +
Sbjct: 705 YIKFSKLHCF-PKLSDEAKKVITREYVKMRQGNFQTSNLDELEHAQEDDDDDLYYQSSGT 763
Query: 358 ----VTTRQLESLVRLTQDI 373
V++R + S++R++ +
Sbjct: 764 RMIYVSSRMISSIIRISVSL 783
Score = 66.9 bits (163), Expect = 2e-11
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 17/91 (18%)
Query: 359 TTRQLESLVRLTQDIQAEPNLFKLLVNSLCPSIFGHEMVKAGLLLALFGG---------- 408
+ Q+ ++ L+++ P ++++L++S PSI VK GLL LF G
Sbjct: 424 SDLQVYKILELSRN----PMIYRILLDSFAPSIKARNNVKIGLLCQLFSGNKNSSDFNKS 479
Query: 409 ---CHSTNGSRGDAHVLIVGDPGLGKSQMLH 436
C+ + RG +VL+ GDPG KSQ+LH
Sbjct: 480 PDACYKVDNFRGIINVLLCGDPGTAKSQLLH 510
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 38.7 bits (90), Expect = 0.009
Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 11/87 (12%)
Query: 181 QALLEAMEQQSISIAKASVVCSLPARTSVIAAANP-----VGGHYNRAKTVAENL----- 230
AL E +E SISI++AS PAR ++AA NP GG + + +
Sbjct: 313 DALREPIEDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWN 372
Query: 231 RMGQALLSRFDL-VFILLDNPDEHLDT 256
++ L R DL V + L P++ L T
Sbjct: 373 KLSGPFLDRIDLSVEVPLLPPEKLLST 399
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 35.6 bits (83), Expect = 0.037
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 181 QALLEAMEQQSISIAKASVVCSLPARTSVIAAANPVG-GHYNRA--------KTVAENL- 230
++L + +E I+I++A + PAR ++AA NP G+ + + L
Sbjct: 124 ESLRQPLEDGEITISRARAKVTFPARFQLVAAMNPCPCGYLGDPDKRCRCTPRQIRRYLS 183
Query: 231 RMGQALLSRFDLVF 244
R+ LL R DL
Sbjct: 184 RLSGPLLDRIDLQV 197
Score = 30.2 bits (69), Expect = 2.3
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 16/58 (27%)
Query: 391 IFGHEMVKAGLLLALFGGCHSTNGSRGDAHVLIVGDPGLGKSQMLHACCAAKKFISVL 448
+ G E K L +A GG H ++L++G PG GK+ ML AK+ +L
Sbjct: 5 VKGQEQAKRALEIAAAGG-H---------NLLMIGPPGSGKT-ML-----AKRLPGIL 46
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 35.7 bits (82), Expect = 0.074
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 182 ALLEAMEQQSISIAKASVVCSLPARTSVIAAANPV-GGHY--NRAKTVAENL-----RMG 233
AL E +E I +++ + PAR ++AA NP GHY N + E R+
Sbjct: 313 ALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLS 372
Query: 234 QALLSRFDL 242
L RFDL
Sbjct: 373 GPFLDRFDL 381
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 35.3 bits (82), Expect = 0.11
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 181 QALLEAMEQQSISIAKASVVCSLPARTSVIAAANP-VGGHY---NRAKTVAENLRM---- 232
+AL E +E I I++A + PAR ++AA NP G+ R +
Sbjct: 301 EALREPLENGKIIISRAGSKVTYPARFQLVAAMNPCPCGNLGAPLRRCPCSPRQIKRYLN 360
Query: 233 --GQALLSRFDLV 243
L R DL+
Sbjct: 361 KLSGPFLDRIDLM 373
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 33.3 bits (77), Expect = 0.12
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 182 ALLEAMEQQSISIAKASVVCSLPARTSVIAAANPV 216
ALLEAM+++ ++I + LP V+A NP+
Sbjct: 81 ALLEAMQERQVTIGGETH--PLPEPFFVLATQNPI 113
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 33.7 bits (78), Expect = 0.20
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 414 GSRGDAHVLIVGDPGLGKSQMLHACCAA 441
+GD + + G+ G GKS +L A CAA
Sbjct: 34 AGKGDRFLYLWGESGSGKSHLLQAACAA 61
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 33.9 bits (78), Expect = 0.22
Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 18/89 (20%)
Query: 390 SIFGHEMVKAGLLLALFGGCHSTNGSRGDAHVLIVGDPGLGKSQMLHACCAAKKF-ISVL 448
+I GHE +K + ++ AH +IVG+ G+GKS + AK+ + +L
Sbjct: 5 TIIGHENIKNRIKNSI------IKNRFSHAH-IIVGEDGIGKSLL------AKEIALKIL 51
Query: 449 QKKAEVQSRSVFTVTELKQLATSANISVD 477
K Q R + E K +I VD
Sbjct: 52 GKS---QQREYVDIIEFK-PINKKSIGVD 76
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 33.1 bits (76), Expect = 0.46
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 415 SRGDAHVLIVGDPGLGKS---QMLHACCAAKK---FISV 447
+ VLI+G+ G GK +++HA A + FI+
Sbjct: 98 APSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAF 136
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 32.8 bits (75), Expect = 0.51
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 10/48 (20%)
Query: 387 LCPSIFGHEMVKAGLLLALFGGCHSTNGSRGDAHVLIVGDPGLGKSQM 434
L + G E V LLAL G HVL+ G PG+GK+ +
Sbjct: 22 LEKVVVGDEEVIELALLALLAG----------GHVLLEGPPGVGKTLL 59
>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family.
Members of this protein family have two copies of the
ABC transporter ATP-binding cassette, but are found
outside the common ABC transporter operon structure that
features integral membrane permease proteins and
substrate-binding proteins encoded next to the
ATP-binding cassette (ABC domain) protein. The member
protein ChvD from Agrobacterium tumefaciens was
identified as both a candidate to interact with VirB8,
based on yeast two-hybrid analysis, and as an apparent
regulator of VirG. The general function of this protein
family is unknown.
Length = 552
Score = 32.6 bits (75), Expect = 0.76
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 224 KTVAENLRMG----QALLSRFDLVFILLDNPDEHLDTLLSEHVMASL 266
KTV EN+ G + L RF+ + PD +D LL+E A L
Sbjct: 83 KTVRENVEEGVAEIKDALDRFNEISAKFAEPDADMDALLAE--QAEL 127
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 32.5 bits (74), Expect = 0.84
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 402 LLALFGGCHSTNGSRGDAHVLIVGDPGLGKSQMLHACCAA 441
L AL T RG A +L+VG+ G+GKS+++H
Sbjct: 489 LEALRRRWRDTVAGRGRA-ILVVGEAGIGKSRLVHELVEK 527
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 31.6 bits (73), Expect = 1.0
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 415 SRGDA--HVLIVGDPGLGKSQMLH 436
RG+A HVL+ G PGLGK+ + +
Sbjct: 45 KRGEALDHVLLYGPPGLGKTTLAN 68
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 31.8 bits (72), Expect = 1.1
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 417 GDAHVLIVGDPGLGKSQMLH 436
G VL+VGD G+GKS ++H
Sbjct: 20 GQVRVLVVGDSGVGKSSLVH 39
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 31.6 bits (73), Expect = 1.2
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 223 AKTVAENLRMG----QALLSRFDLVFILLDNPDEHLDTLLSEHVMASL 266
KTV EN+ G +A L RF+ ++ PD D L +E L
Sbjct: 84 EKTVRENVEEGVAEVKAALDRFNEIYAAYAEPDADFDALAAE--QGEL 129
>gnl|CDD|234681 PRK00182, tatB, sec-independent translocase; Provisional.
Length = 160
Score = 30.6 bits (69), Expect = 1.2
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 226 VAENLRMG-QALLSRFDLVFILLDNPDEHLDTLLSEHVMASLSGFQSNRNPSHSTQSFTE 284
+A RMG + +++ L D D LD + +MA + ++ R S
Sbjct: 69 IASYRRMGPKTAITK-----ALFDGDDSFLDDFDPKKIMADGTEGEAQRQQQASAGRADN 123
Query: 285 NPNSVQSDIPLSE 297
N N V S+
Sbjct: 124 NANVVTRPADGSQ 136
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 30.4 bits (68), Expect = 1.5
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 420 HVLIVGDPGLGKSQMLHACC 439
+LIVG PG GK+ + A
Sbjct: 4 VILIVGPPGSGKTTLARALA 23
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 29.8 bits (67), Expect = 2.3
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 415 SRGDAHVLIVGDPGLGKSQMLHA 437
++L+ G PG GK+ + A
Sbjct: 16 LPPPKNLLLYGPPGTGKTTLARA 38
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 29.6 bits (68), Expect = 2.6
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 418 DAHVLIVGDPGLGKS---QMLHACC--AAKKFISV 447
DA VLI G+ G GK + +H A F++V
Sbjct: 22 DATVLITGESGTGKELFARAIHQLSPRADGPFVAV 56
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 30.5 bits (70), Expect = 2.7
Identities = 12/18 (66%), Positives = 14/18 (77%), Gaps = 2/18 (11%)
Query: 416 RGDA--HVLIVGDPGLGK 431
RG+A HVL+ G PGLGK
Sbjct: 47 RGEALDHVLLYGPPGLGK 64
>gnl|CDD|211833 TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium
transferase. In the archaea and eukaryotes, the
conversion of the mischarged serine to selenocysteine
(Sec) on its tRNA is accomplished in two steps. This
enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase,
acts second, after a phosphophorylation step catalyzed
by a homolog of the bacterial SelA protein [Protein
synthesis, tRNA aminoacylation].
Length = 444
Score = 30.4 bits (69), Expect = 2.7
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 471 SANISVDNFFTFLTSLNDQGF--LLKKGKQLYQLMSAKKFISVLQKKAEVQSRSVFTVTE 528
SA+ S+D T L SL +G+ LLK+ K++Y+ + LQK AE + E
Sbjct: 304 SASPSLDVLITLL-SLGSKGYLELLKERKEMYKYLKEL-----LQKLAERHGERLLDTPE 357
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 29.9 bits (67), Expect = 2.9
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 421 VLIVGDPGLGKSQMLHACC 439
VL++GD G+GKS ++H C
Sbjct: 3 VLVLGDSGVGKSSLVHLLC 21
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 30.4 bits (70), Expect = 3.1
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 421 VLIVGDPGLGKSQ-MLHACCA-AKKFISVL 448
VLI GDPG+GKS +L A VL
Sbjct: 83 VLIGGDPGIGKSTLLLQVAARLAAAGGKVL 112
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 30.3 bits (69), Expect = 3.1
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 421 VLIVGDPGLGKSQML 435
+LI GDPG+GKS +L
Sbjct: 96 ILIGGDPGIGKSTLL 110
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 30.5 bits (69), Expect = 3.4
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 230 LRMGQALLSRFDLVFILLDNPDEHLD 255
L + QAL+ R DL +LLD P HLD
Sbjct: 158 LNLAQALICRSDL--LLLDEPTNHLD 181
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 30.2 bits (69), Expect = 3.4
Identities = 13/23 (56%), Positives = 17/23 (73%), Gaps = 2/23 (8%)
Query: 416 RGDA--HVLIVGDPGLGKSQMLH 436
RG+A HVL+ G PGLGK+ + H
Sbjct: 48 RGEALDHVLLFGPPGLGKTTLAH 70
>gnl|CDD|236769 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 30.0 bits (68), Expect = 4.2
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 418 DAHVLIVGDPGLGKSQMLHAC 438
DA +LI GD G GK + +AC
Sbjct: 227 DAPLLITGDTGTGKDLLAYAC 247
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 29.3 bits (66), Expect = 4.2
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 416 RGDAHVLIVGDPGLGKSQMLHA 437
H+LI G G GKS L+
Sbjct: 36 VKMPHLLIAGATGSGKSTFLNT 57
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 29.6 bits (67), Expect = 4.6
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 414 GSRGDAHVLIVGDPGLGKSQMLHACCAA 441
G D + G+ G G+S +L A A
Sbjct: 38 GPVADRFFYLWGEAGSGRSHLLQALVAD 65
>gnl|CDD|224410 COG1493, HprK, Serine kinase of the HPr protein, regulates
carbohydrate metabolism [Signal transduction
mechanisms].
Length = 308
Score = 29.5 bits (67), Expect = 5.1
Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 11/44 (25%)
Query: 389 PSIFGHEMVKAGLLLALFGGCHSTNGSRGDAHVLIVGDPGLGKS 432
+ G+LL +FG G VLI G G GKS
Sbjct: 127 SRPLAERVNVHGVLLDIFG--------VG---VLITGPSGAGKS 159
>gnl|CDD|217478 pfam03294, Pox_Rap94, RNA polymerase-associated transcription
specificity factor, Rap94.
Length = 796
Score = 29.7 bits (67), Expect = 5.6
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 21/77 (27%)
Query: 2 IISYKKDGPTDTKIKSCLDFIERH-----NHLYNVAEIEERRCYLVDIKVLMNDQIFNDQ 56
I +Y KD D K S DFI + N+LYNV+ I + DI++L
Sbjct: 15 IKAYIKDPNIDPK--SYDDFISENKNIFVNNLYNVSTITDE-----DIRLL--------- 58
Query: 57 WKTFLQNLSNEPQHTIN 73
+ T QN + Q I+
Sbjct: 59 YATIEQNPDADDQTLIS 75
>gnl|CDD|184766 PRK14610, PRK14610, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 283
Score = 29.3 bits (66), Expect = 5.6
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 288 SVQSDIPLSERLKP----GPGEELPLIPAPLLHKYLAYAR---KYVSKPE 330
SV SD+P K G GE++ L+P L Y+ K++S +
Sbjct: 130 SVGSDVPACLDSKTLFVRGIGEDILLLPDLSLPTYVVLVAPKGKFLSTRK 179
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 29.6 bits (67), Expect = 6.0
Identities = 10/16 (62%), Positives = 13/16 (81%), Gaps = 1/16 (6%)
Query: 420 HVLIVGDPGLGKSQML 435
HV+++G PG GKS ML
Sbjct: 52 HVMMIGSPGTGKS-ML 66
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.6 bits (66), Expect = 6.4
Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 14/104 (13%)
Query: 414 GSRGDAHVLIVGDPGLGKSQMLHACCA-AKKFISVLQKKAEVQSRSVFTVTELKQLATSA 472
+ + L+VG+ G GK+ M+ ++V+ K + + + +T
Sbjct: 460 NIQNNEPTLLVGETGTGKTTMIQYLALKLHFKLTVINKSQQTEMSDDLGGYKPINGSTLG 519
Query: 473 NISVDNFFTFLTSLNDQGFLLKKGKQLYQLMSAKKFISVLQKKA 516
+ F + + F +KK KFI + Q+ +
Sbjct: 520 LPLHERFID----IFEGTFSMKK---------NIKFICMEQRVS 550
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 29.2 bits (66), Expect = 6.5
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 421 VLIVGDPGLGKSQMLHACCAA 441
+ I G GLGK+ +L A
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNE 136
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 29.1 bits (66), Expect = 6.6
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 420 HVLIVGDPGLGKSQMLH 436
H+LIVG G GK+Q L
Sbjct: 17 HILIVGTTGTGKTQALR 33
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 29.1 bits (66), Expect = 6.9
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 421 VLIVGDPGLGKSQML--HACCAAKKFISVL 448
+LI GDPG+GKS +L A AK+ VL
Sbjct: 85 ILIGGDPGIGKSTLLLQVAARLAKRGGKVL 114
>gnl|CDD|237748 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion
protein; Provisional.
Length = 230
Score = 28.8 bits (64), Expect = 7.0
Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 6/101 (5%)
Query: 441 AKKFISVLQKKAEVQSRSVFTVTELKQLATSANISVDNFFTFLTSLNDQGFLLKKGKQLY 500
AKKF+S Q + + V L++ I+ + T L + L + K
Sbjct: 113 AKKFLSQFQSTTITKPKKVLINEVLQE----KTINQNEEKTSLQNEKVLSPELSEEKSDS 168
Query: 501 QLMSAKKFISVLQKKA--EVQSRSVFTVTELKQLATSANIS 539
+L + + + +KK E S + ELK+LA I
Sbjct: 169 ELETQPQKTQLKEKKPSIEHIDLSKMLLKELKKLAKEHKIP 209
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 29.2 bits (66), Expect = 7.8
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 413 NGSRGDAHVLIVGDPGLGK---SQMLHACC--AAKKFISV 447
++ D+ VLI+G+ G GK ++ +H A FI++
Sbjct: 263 RIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAI 302
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 28.9 bits (65), Expect = 8.7
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 235 ALLSRFDLVFILLDNPDEHLDTLLSEHVMASL 266
ALL+ + +LLD P EHLD ++ ++ L
Sbjct: 485 ALLADAPI--LLLDEPTEHLDAETADELLEDL 514
>gnl|CDD|147308 pfam05059, Orbi_VP4, Orbivirus VP4 core protein. Orbiviruses are
double stranded RNA retroviruses of which the bluetongue
virus is a member. The core of bluetongue virus (BTV) is
a multienzyme complex composed of two major proteins
(VP7 and VP3) and three minor proteins (VP1, VP4 and
VP6) in addition to the viral genome. VP4 has been shown
to perform all RNA capping activities and has both
methyltransferase type 1 and type 2 activities
associated with it.
Length = 642
Score = 28.9 bits (65), Expect = 8.9
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 2 IISYKKDGPTDTKIKSCLDFI 22
I Y DGPTD K+ S LD+I
Sbjct: 166 IGPYSDDGPTDEKLVSMLDYI 186
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 29.0 bits (65), Expect = 9.0
Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 421 VLIVGDPGLGKSQMLH--ACCAAKKFISVLQKKAE 453
+LI GDPG+GKS +L AC AK + VL E
Sbjct: 97 ILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE 131
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 29.0 bits (65), Expect = 9.7
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 420 HVLIVGDPGLGKSQMLHA 437
+VL++G+PG+GKS + A
Sbjct: 39 NVLLIGEPGVGKSMLAKA 56
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 27.9 bits (63), Expect = 9.7
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 415 SRGDAHVLIVGDPGLGKSQMLHACC 439
GD +LI G G GKS + A
Sbjct: 25 KPGD-RLLITGPSGTGKSSLFRALA 48
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 28.8 bits (65), Expect = 9.9
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 418 DAHVLIVGDPGLGKSQMLHA 437
D H+ I G PG GKS L
Sbjct: 810 DGHLAIFGSPGYGKSTFLQT 829
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
0.319 0.132 0.379
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,198,289
Number of extensions: 2909701
Number of successful extensions: 3009
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2992
Number of HSP's successfully gapped: 73
Length of query: 613
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 510
Effective length of database: 6,369,140
Effective search space: 3248261400
Effective search space used: 3248261400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (28.1 bits)