RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780829|ref|YP_003065242.1| ATP-dependent protease
ATP-binding subunit [Candidatus Liberibacter asiaticus str. psy62]
(437 letters)
>gnl|CDD|31413 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 589 bits (1521), Expect = e-169
Identities = 255/445 (57%), Positives = 329/445 (73%), Gaps = 16/445 (3%)
Query: 6 NFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVG 65
+PREIVSELDRYIIGQ +AK+AVAIALRNRWRR QL +LRDE+ PKNIL++GPTGVG
Sbjct: 3 EMTPREIVSELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVG 62
Query: 66 KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQ 125
KT I+RRLA+LAGAPFIKVE TKFTE+GYVGR+VE IIRDLV++A+ +VRE + ++V+++
Sbjct: 63 KTEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKLVREEKIEKVKDK 122
Query: 126 ASINAEERILDALVGKT-----------ATSNTREVFRKKLRDGEISDKEIDIEVADTSS 174
A AEERILDALV +S TRE FRKKLR+GE+ DKEI+IEVAD
Sbjct: 123 AEELAEERILDALVPPAKNFWGQSENKQESSATREKFRKKLREGELDDKEIEIEVADKGP 182
Query: 175 DISNFDIPG--GASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDT 232
F+I G G NL ++F + G +KKK ++ V++ L+ +E+D+LID +
Sbjct: 183 --PGFEIMGPPGMEEMTNNLQDMFGNLGG-KKKKKRKLKVKEAKKLLIEEEADKLIDQEE 239
Query: 233 VHRDSIQMVENYGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSIN 292
+ +++I E GIVF+DE DKI R G VSREGVQRDLLPLVEGS+VSTKYG +
Sbjct: 240 IKQEAIDAAEQNGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVK 299
Query: 293 TDHILFIASGAFHVSRPADLLPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKEL 352
TDHILFIASGAFHV++P+DL+PE+QGRFP+RV L +L K DF ILT+ +++LI QYK L
Sbjct: 300 TDHILFIASGAFHVAKPSDLIPELQGRFPIRVELDALTKEDFERILTEPKASLIKQYKAL 359
Query: 353 MKTEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTV 412
+KTEG+ L+FT+D+I +A++A +N +IGARRL TV+ER+LEDISF A D+ + V
Sbjct: 360 LKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARRLHTVLERLLEDISFEAPDMSGQKV 419
Query: 413 VIDAEYVRLHIGDFPSETDMYHFIL 437
IDAEYV +GD + D+ FIL
Sbjct: 420 TIDAEYVEEKLGDLVANEDLSRFIL 444
>gnl|CDD|35964 KOG0745, KOG0745, KOG0745, Putative ATP-dependent Clp-type protease
(AAA+ ATPase superfamily) [Posttranslational
modification, protein turnover, chaperones].
Length = 564
Score = 109 bits (274), Expect = 1e-24
Identities = 75/240 (31%), Positives = 108/240 (45%), Gaps = 70/240 (29%)
Query: 245 GIVFLDEFDKIVARDSGNGIG--VSREGVQRDLLPLVEGSSVS--------TKYGS---I 291
GIVFLDE DKI + VS EGVQ+ LL L+EG+ V+ G I
Sbjct: 293 GIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQI 352
Query: 292 NTDHILFIASGAF-----HVSR-------------------------------------- 308
+T +ILFIASGAF +SR
Sbjct: 353 DTTNILFIASGAFVGLDKIISRRLDDKSLGFGAPSSKGVRANMATKSGVENDAEKRDELL 412
Query: 309 ----PADL-----LPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGII 359
DL +PE GRFPV V L SL++ +LT+ ++ L QYK+L + +
Sbjct: 413 EKVESGDLISFGMIPEFVGRFPVLVPLHSLDEDQLVRVLTEPKNALGKQYKKLFGMDNVE 472
Query: 360 LDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVIDAEYV 419
L FTE +++A+A +A+ + GAR L++++E +L + F K V++D E V
Sbjct: 473 LHFTEKALEAIAQLALKRKT-----GARGLRSILESLLLEAMFEVPGSDIKAVLVDEEAV 527
Score = 75.8 bits (186), Expect = 2e-14
Identities = 47/165 (28%), Positives = 77/165 (46%), Gaps = 51/165 (30%)
Query: 9 PREIVSELDRYIIGQQDAKRAVAIALRNRWRR---------------------------- 40
P+EI LD++++GQ+ AK+ +++A+ N ++R
Sbjct: 136 PKEICEYLDKFVVGQEKAKKVLSVAVYNHYKRIYHNEPSRQKELAEASKSAKDRDNPIEL 195
Query: 41 ------QQLPADLRD------------ELMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82
Q P + R EL N+LL+GPTG GKT +++ LAR+ PF
Sbjct: 196 EISESNAQWPNNQRQIAKALDEDDEDVELEKSNVLLLGPTGSGKTLLAQTLARVLDVPFA 255
Query: 83 KVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRR-----DEV 122
+ T T+ GYVG +VE +I+ L+ A V ++++ DEV
Sbjct: 256 ICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEV 300
>gnl|CDD|31412 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 106 bits (267), Expect = 1e-23
Identities = 70/230 (30%), Positives = 113/230 (49%), Gaps = 61/230 (26%)
Query: 245 GIVFLDEFDKIVARDSGNGIG---VSREGVQRDLLPLVEGSSVST-----------KYGS 290
GI+++DE DKI AR S N VS EGVQ+ LL ++EG+ S ++
Sbjct: 164 GIIYIDEIDKI-ARKSENPSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPQQEFIQ 222
Query: 291 INTDHILFIASGAF-----HVSR------------------------------PADLL-- 313
++T +ILFI GAF + + P DL+
Sbjct: 223 VDTSNILFICGGAFAGLEKIIKKRLGKKGIGFGAEVKSKSKKKEEGELLKQVEPEDLVKF 282
Query: 314 ---PEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDAL 370
PE GR PV L+ L++ ILT+ ++ L+ QY++L + +G+ L+FTE+++ A+
Sbjct: 283 GLIPEFIGRLPVIATLEELDEDALVQILTEPKNALVKQYQKLFEMDGVELEFTEEALKAI 342
Query: 371 ADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQE-KTVVIDAEYV 419
A A+ + GAR L++++E +L D+ F L++ + VVI E V
Sbjct: 343 AKKAIERKT-----GARGLRSIIEELLLDVMFELPSLEDVEKVVITEEVV 387
Score = 98.7 bits (246), Expect = 3e-21
Identities = 45/104 (43%), Positives = 67/104 (64%), Gaps = 1/104 (0%)
Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRD-ELMPKNILLVGPTGVGK 66
+P+EI + LD Y+IGQ+ AK+ +++A+ N ++R D D EL NILL+GPTG GK
Sbjct: 51 TPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGK 110
Query: 67 TAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
T +++ LA++ PF + T TE GYVG +VE I+ L+ A
Sbjct: 111 TLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAA 154
>gnl|CDD|31416 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 50.7 bits (121), Expect = 7e-07
Identities = 36/109 (33%), Positives = 54/109 (49%), Gaps = 14/109 (12%)
Query: 8 SPREIVSELDRYI-----IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPT 62
+PRE E+ I IGQ++AKR + + + P D PKN+L GP
Sbjct: 106 TPREEDREIISDITLDDVIGQEEAKRKCRLIME----YLENPERFGD-WAPKNVLFYGPP 160
Query: 63 GVGKTAISRRLARLAGAPFIKVEVTKFTEIG-YVGRNVEQIIRDLVDVA 110
G GKT +++ LA A P + V+ T+ IG +VG + I +L + A
Sbjct: 161 GTGKTMMAKALANEAKVPLLLVKATEL--IGEHVGDGARR-IHELYERA 206
>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 = 48.7 bits (116), Expect = 3e-06
Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 17/89 (19%)
Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLA--- 77
+GQ++A A+ AL PKN+LL GP G GKT ++R +A
Sbjct: 1 VGQEEAIEALREALELP--------------PPKNLLLYGPPGTGKTTLARAIANELFRP 46
Query: 78 GAPFIKVEVTKFTEIGYVGRNVEQIIRDL 106
GAPF+ + + E V + L
Sbjct: 47 GAPFLYLNASDLLEGLVVAELFGHFLVRL 75
Score = 30.2 bits (68), Expect = 1.1
Identities = 19/112 (16%), Positives = 42/112 (37%), Gaps = 20/112 (17%)
Query: 217 PELMRDESDRLIDMDTVHRDSIQMVE--NYGIVFLDEFDKIVARDSGNGIGVSREGVQRD 274
+L+ + + R ++ E G++F+DE D + G Q
Sbjct: 56 SDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL------------SRGAQNA 103
Query: 275 LLPLVEGSSVSTKYGSINTDHILFIASGAFHVSRPADLLPEIQGRFPVRVHL 326
LL ++E + I+ +++ I + + DL + R +R+ +
Sbjct: 104 LLRVLETLNDLR----IDRENVRVIGAT--NRPLLGDLDRALYDRLDIRIVI 149
>gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 47.0 bits (111), Expect = 1e-05
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 16/84 (19%)
Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKT 67
+I SEL++ ++G ++ +AL L ++LL GP GVGKT
Sbjct: 14 ILGKIRSELEKVVVGDEEVIELALLAL----------------LAGGHVLLEGPPGVGKT 57
Query: 68 AISRRLARLAGAPFIKVEVTKFTE 91
++R LAR G PF++++ T
Sbjct: 58 LLARALARALGLPFVRIQCTPDLL 81
>gnl|CDD|35953 KOG0734, KOG0734, KOG0734, AAA+-type ATPase containing the
peptidase M41 domain [Posttranslational modification,
protein turnover, chaperones].
Length = 752
Score = 46.9 bits (111), Expect = 1e-05
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
+PK +LLVGP G GKT ++R +A AG PF ++F E+ +VG + +RDL A
Sbjct: 336 LPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEM-FVGVGARR-VRDLFAAA 392
>gnl|CDD|35952 KOG0733, KOG0733, KOG0733, Nuclear AAA ATPase (VCP subfamily)
[Posttranslational modification, protein turnover,
chaperones].
Length = 802
Score = 45.0 bits (106), Expect = 4e-05
Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 9/94 (9%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAIN 112
P+ +LL GP G GKT+++ +A G PF+ + + G G + E+ IR+L D A +
Sbjct: 223 PRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVS-GVSGES-EKKIRELFDQAKS 280
Query: 113 ----IVRESRRDEV---REQASINAEERILDALV 139
IV D + RE+A E RI+ L+
Sbjct: 281 NAPCIVFIDEIDAITPKREEAQREMERRIVAQLL 314
Score = 33.4 bits (76), Expect = 0.11
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVE 85
P +LL GP G GKT +++ +A AGA FI V+
Sbjct: 545 PSGVLLCGPPGCGKTLLAKAVANEAGANFISVK 577
>gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 43.7 bits (104), Expect = 1e-04
Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 17/94 (18%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVR 115
+LL GP G GKT +++ +A+ GAPFI++ ++ YVG E+ +R+L + A +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVG-ESEKRLRELFEAA----K 54
Query: 116 ESRR-----DEV------REQASINAEERILDAL 138
+ DE+ R + R+++ L
Sbjct: 55 KLAPCVIFIDEIDALAGSRGSGGDSESRRVVNQL 88
Score = 37.2 bits (87), Expect = 0.010
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 13/82 (15%)
Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHILFIASGAFH 305
++F+DE D + G SR V LL ++G + + ++ IA+
Sbjct: 60 VIFIDEIDALAGSRGSGGDSESRR-VVNQLLTELDG-------FTSSLSKVIVIAAT--- 108
Query: 306 VSRPADLLPEI-QGRFPVRVHL 326
+RP L P + +GRF +
Sbjct: 109 -NRPDKLDPALLRGRFDRIIEF 129
>gnl|CDD|35956 KOG0737, KOG0737, KOG0737, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 386
Score = 43.0 bits (101), Expect = 2e-04
Identities = 20/39 (51%), Positives = 26/39 (66%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91
PK ILL GP G GKT +++ +A+ AGA FI V V+ T
Sbjct: 127 PKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTS 165
>gnl|CDD|177080 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 42.0 bits (99), Expect = 3e-04
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91
PK +LLVGP G GKT +++ +A A PF + ++F E
Sbjct: 216 PKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVE 254
>gnl|CDD|35950 KOG0731, KOG0731, KOG0731, AAA+-type ATPase containing the
peptidase M41 domain [Posttranslational modification,
protein turnover, chaperones].
Length = 774
Score = 42.0 bits (98), Expect = 3e-04
Identities = 24/54 (44%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDL 106
PK +LLVGP G GKT +++ +A AG PF V ++F E+ +VG + +RDL
Sbjct: 344 PKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEM-FVGVGASR-VRDL 395
>gnl|CDD|30672 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 41.8 bits (98), Expect = 4e-04
Identities = 29/101 (28%), Positives = 45/101 (44%), Gaps = 11/101 (10%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVE---VTKFTEIGYVG------RNVEQI 102
PK I++ GPT GKTA++ LA+ G I ++ V + +IG V
Sbjct: 2 KPKLIVIAGPTASGKTALAIALAKRLGGEIISLDSMQVYRGLDIGTAKPSLEELAGVPHH 61
Query: 103 IRDLVDVAINI-VRESRRDEVREQASINAEERILDALVGKT 142
+ D+ D + E +RD + I A ++ LVG T
Sbjct: 62 LIDIRDPTESYSAAEFQRDALAAIDDILARGKLP-ILVGGT 101
>gnl|CDD|30813 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 41.9 bits (98), Expect = 4e-04
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 51 LMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
+PK +LLVGP G GKT +++ +A AG PF + + F E+ +VG + +RDL + A
Sbjct: 181 KIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM-FVGVGASR-VRDLFEQA 238
>gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 786
Score = 41.4 bits (97), Expect = 4e-04
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 10 REIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPK-NILLVGPTGVGKTA 68
+ L + +IGQ +A AV+ A+R + A L D P + L +GPTGVGKT
Sbjct: 483 LNLERRLKKRVIGQDEAVEAVSDAIR------RARAGLGDPNRPIGSFLFLGPTGVGKTE 536
Query: 69 ISRRLAR 75
+++ LA
Sbjct: 537 LAKALAE 543
Score = 30.7 bits (69), Expect = 0.75
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 55 NILLVGPTGVGKTAISRRLAR 75
N +LVG GVGKTAI LA+
Sbjct: 193 NPVLVGEPGVGKTAIVEGLAQ 213
>gnl|CDD|36269 KOG1051, KOG1051, KOG1051, Chaperone HSP104 and related
ATP-dependent Clp proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 898
Score = 40.8 bits (95), Expect = 8e-04
Identities = 30/99 (30%), Positives = 50/99 (50%), Gaps = 17/99 (17%)
Query: 12 IVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISR 71
+ L +IGQ +A A+A A+R + A L+D L +GP GVGKT +++
Sbjct: 556 LEERLHERVIGQDEAVAAIAAAIR------RSRAGLKDPNPDAWFLFLGPDGVGKTELAK 609
Query: 72 RLARL---AGAPFIKVEVTKFTEI--------GYVGRNV 99
LA + FI++++++F E+ GYVG+
Sbjct: 610 ALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEE 648
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyses 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 = 39.8 bits (94), Expect = 0.001
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 16/54 (29%)
Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRL 73
+ GQ+ AKRA+ IA N+L++GP G GKT +++RL
Sbjct: 5 VKGQEQAKRALEIAAAGG----------------HNLLMIGPPGSGKTMLAKRL 42
>gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 39.0 bits (91), Expect = 0.002
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFI 82
NI+L+G G GK+ I R LA+ PFI
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|35948 KOG0729, KOG0729, KOG0729, 26S proteasome regulatory complex,
ATPase RPT1 [Posttranslational modification, protein
turnover, chaperones].
Length = 435
Score = 38.8 bits (90), Expect = 0.003
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
PK +LL GP G GKT +R +A A FI+V ++ + YVG +++R+L ++A
Sbjct: 211 PKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSELVQ-KYVGEGA-RMVRELFEMA 266
>gnl|CDD|30812 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 38.6 bits (89), Expect = 0.003
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT--EIGYVGRNVEQIIRD 105
PK +LL GP G GKT +++ +A + + FI V+ ++ +G +N+ ++
Sbjct: 276 PKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEK 330
>gnl|CDD|31415 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 37.5 bits (87), Expect = 0.007
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
PK +LL GP G GKT +++ +A A FI+V ++ + Y+G +++R+L ++A
Sbjct: 185 PKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQ-KYIGEG-ARLVRELFELA 240
Score = 28.7 bits (64), Expect = 3.0
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLV 279
I+F+DE D I A+ +G RE VQR +L L+
Sbjct: 247 IIFIDEIDAIGAKRFDSGTSGDRE-VQRTMLELL 279
>gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP..
Length = 154
Score = 37.5 bits (87), Expect = 0.007
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFI 82
NI+L+G G GKT + R LA+ G PF+
Sbjct: 1 NIVLIGMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 36.9 bits (85), Expect = 0.010
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 16/87 (18%)
Query: 9 PREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTA 68
+ SE +IG+ + + + R+Q+ A L +L++G TG GK
Sbjct: 69 RPYLKSEALDDLIGESPSLQEL---------REQIKAYAPSGL---PVLIIGETGTGKEL 116
Query: 69 ISRRL----ARLAGAPFIKVEVTKFTE 91
+R + AR A APFI ++E
Sbjct: 117 FARLIHALSARRAEAPFIAFNCAAYSE 143
>gnl|CDD|35946 KOG0727, KOG0727, KOG0727, 26S proteasome regulatory complex,
ATPase RPT3 [Posttranslational modification, protein
turnover, chaperones].
Length = 408
Score = 36.9 bits (85), Expect = 0.011
Identities = 26/90 (28%), Positives = 50/90 (55%), Gaps = 7/90 (7%)
Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAP 80
+ +Q+ + AV + L + +Q+ D P+ +LL GP G GKT +++ +A A
Sbjct: 162 VQKQEIREAVELPLTHADLYKQIGID-----PPRGVLLYGPPGTGKTMLAKAVANHTTAA 216
Query: 81 FIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
FI+V ++F + Y+G +++RD+ +A
Sbjct: 217 FIRVVGSEFVQ-KYLGEG-PRMVRDVFRLA 244
>gnl|CDD|177027 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 36.2 bits (84), Expect = 0.019
Identities = 32/99 (32%), Positives = 50/99 (50%), Gaps = 21/99 (21%)
Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRL 73
L + IIGQ +A AV+ A+R R R L++ P + L GPTGVGKT +++ L
Sbjct: 506 TLHKRIIGQDEAVVAVSKAIR-RAR-----VGLKNPNRPIASFLFSGPTGVGKTELTKAL 559
Query: 74 ARL---AGAPFIKVEVTKFTE-----------IGYVGRN 98
A + I+++++++ E GYVG N
Sbjct: 560 ASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYN 598
Score = 28.9 bits (65), Expect = 2.6
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 55 NILLVGPTGVGKTAISRRLARL 76
N +L+G GVGKTAI+ LA+
Sbjct: 202 NPILIGEPGVGKTAIAEGLAQR 223
>gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 35.9 bits (83), Expect = 0.020
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
L +L + LVGP GVGKT++ + +A+ G F+++ +
Sbjct: 344 LTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISL 383
>gnl|CDD|35949 KOG0730, KOG0730, KOG0730, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 693
Score = 36.1 bits (83), Expect = 0.020
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
PK +LL GP G GKT +++ LA AG F+ V+ + YVG + E+ IR++ A
Sbjct: 468 PKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELF-SKYVGES-ERAIREVFRKA 523
Score = 31.4 bits (71), Expect = 0.50
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
P+ +LL GP G GKT + R +A GA +
Sbjct: 218 PRGLLLYGPPGTGKTFLVRAVANEYGAFLFLING 251
>gnl|CDD|143926 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 35.8 bits (84), Expect = 0.023
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 53 PKNILLVGPTGVGKTAISRRLARL---AGAPFIKV 84
+L+ G +G GK +R + +L A PF+ V
Sbjct: 22 DATVLITGESGTGKELFARAIHQLSPRADGPFVAV 56
>gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease
PIM1/LON [Posttranslational modification, protein
turnover, chaperones].
Length = 906
Score = 35.7 bits (82), Expect = 0.023
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG--------YVGRN 98
LR + K + VGP GVGKT+I++ +AR F + V T++ YVG
Sbjct: 432 LRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGAM 491
Query: 99 VEQIIRDLVDVAIN 112
+II+ L V
Sbjct: 492 PGKIIQCLKKVKTE 505
>gnl|CDD|177097 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 35.7 bits (82), Expect = 0.026
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 44 PADLRDELMP-KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKF 89
P LR L P + IL++G G G++ + + LA + PFI V + KF
Sbjct: 1620 PFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKF 1666
>gnl|CDD|35871 KOG0652, KOG0652, KOG0652, 26S proteasome regulatory complex,
ATPase RPT5 [Posttranslational modification, protein
turnover, chaperones].
Length = 424
Score = 35.0 bits (80), Expect = 0.047
Identities = 37/132 (28%), Positives = 60/132 (45%), Gaps = 22/132 (16%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAIN 112
PK +L+ GP G GKT ++R A A F+K+ + ++ ++G +++RD A
Sbjct: 205 PKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQM-FIGDGA-KLVRD----AFA 258
Query: 113 IVRESRRDEVREQASINAEERILDALVGK---TATSNTREVFRKKLR-----DGEISDKE 164
+ +E + I +E LDA+ K + + REV R L DG SD
Sbjct: 259 LAKE------KAPTIIFIDE--LDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDR 310
Query: 165 IDIEVADTSSDI 176
+ + A DI
Sbjct: 311 VKVIAATNRVDI 322
>gnl|CDD|35870 KOG0651, KOG0651, KOG0651, 26S proteasome regulatory complex,
ATPase RPT4 [Posttranslational modification, protein
turnover, chaperones].
Length = 388
Score = 34.9 bits (80), Expect = 0.048
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE--IGYVGRNVEQIIRDLVDVA 110
PK +LL GP G GKT ++R +A G F+KV + + IG R + + R +V
Sbjct: 166 PKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYIGESARLIRDMFRYAREVI 225
Query: 111 INIVRESRRDEV 122
I+ D +
Sbjct: 226 PCIIFMDEIDAI 237
>gnl|CDD|35959 KOG0740, KOG0740, KOG0740, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 428
Score = 34.6 bits (79), Expect = 0.057
Identities = 30/96 (31%), Positives = 49/96 (51%), Gaps = 14/96 (14%)
Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELM-----PKNILLVGPTGVGKTAISRRLA 74
I G +DAK+++ A+ LP D + + +LL GP G GKT +++ +A
Sbjct: 155 IAGLEDAKQSLKEAV-------ILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIA 207
Query: 75 RLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
+GA F + + T YVG + E+++R L VA
Sbjct: 208 TESGATFFNISASSLTS-KYVGES-EKLVRALFKVA 241
>gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 952
Score = 34.2 bits (78), Expect = 0.068
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEI--GYVGRNVEQIIRDLVDV 109
+ ILL GP G GKT ++ +A + FI V K E+ Y+G + EQ +RDL +
Sbjct: 700 LRTGILLYGPPGCGKTLLASAIASNSNLRFISV---KGPELLSKYIGAS-EQNVRDLFER 755
Query: 110 A 110
A
Sbjct: 756 A 756
Score = 27.3 bits (60), Expect = 9.2
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 51 LMPKNILLVGPTGVGKTAISRRLA 74
NILL GP G GKT + + L
Sbjct: 429 FRHGNILLNGPKGSGKTNLVKALF 452
>gnl|CDD|32437 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 34.4 bits (79), Expect = 0.068
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT 90
+++L GP G GKT ++R +A A F +
Sbjct: 50 SMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSG 85
>gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 744
Score = 34.2 bits (78), Expect = 0.070
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKV 84
+LL GP G GKTA++ ++A + PF+K+
Sbjct: 541 VLLEGPPGSGKTALAAKIALSSDFPFVKI 569
Score = 30.7 bits (69), Expect = 0.74
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 5/55 (9%)
Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEI--GYVGRNVEQIIRDL 106
K ILL GP G GKT I+R++ ++ A K + EI YVG + E+ +R L
Sbjct: 257 KGILLYGPPGTGKTLIARQIGKMLNAREPK--IVNGPEILNKYVGES-EENVRKL 308
>gnl|CDD|35957 KOG0738, KOG0738, KOG0738, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 491
Score = 34.2 bits (78), Expect = 0.071
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
K +L+VGP G GKT +++ +A G F V + T + G + E+++R L ++A
Sbjct: 246 KGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTS-KWRGES-EKLVRLLFEMA 300
>gnl|CDD|30951 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 34.0 bits (78), Expect = 0.078
Identities = 25/77 (32%), Positives = 32/77 (41%), Gaps = 25/77 (32%)
Query: 9 PREIVSELDRY---------IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLV 59
P I SE+ + GQ+ AKRA+ IA N+LLV
Sbjct: 161 PIPIPSEVIESFSLAPDFKDVKGQEQAKRALEIAAAGG----------------HNLLLV 204
Query: 60 GPTGVGKTAISRRLARL 76
GP G GKT ++ RL L
Sbjct: 205 GPPGTGKTMLASRLPGL 221
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase
/ dimethylallyl transferase synthesizes
isopentenyladensosine 5'-monophosphate, a cytokinin
that induces shoot formation on host plants infected
with the Ti plasmid.
Length = 232
Score = 33.9 bits (78), Expect = 0.086
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 57 LLVGPTGVGKTAISRRLARLAGAPFI 82
L+ G T GKTA + LA+ G P I
Sbjct: 5 LIWGATCTGKTAEAIALAKETGWPVI 30
>gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits..
Length = 150
Score = 33.3 bits (76), Expect = 0.12
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82
I+++G +G GK+ + + LA GAPFI
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates..
Length = 194
Score = 32.5 bits (74), Expect = 0.23
Identities = 36/127 (28%), Positives = 58/127 (45%), Gaps = 22/127 (17%)
Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIGYVGRNVEQIIR--DL 106
ILL+GP G GK + RLA+ G P I E+ TE+ G+ ++ I L
Sbjct: 1 RILLLGPPGSGKGTQAERLAKKYGLPHISTGDLLREEIASGTEL---GKKAKEYIDSGKL 57
Query: 107 V--DVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKE 164
V ++ I +++E + ++ ILD G T + E + L +G DK
Sbjct: 58 VPDEIVIKLLKERLKKPDCKKGF------ILD---GFPRTVDQAEALDELLDEGIKPDKV 108
Query: 165 IDIEVAD 171
I+++V D
Sbjct: 109 IELDVPD 115
>gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 32.6 bits (74), Expect = 0.25
Identities = 15/26 (57%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAG 78
+ I LVGPTGVGKT LA+LA
Sbjct: 203 KRVIALVGPTGVGKTTT---LAKLAA 225
>gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 32.3 bits (73), Expect = 0.25
Identities = 33/171 (19%), Positives = 63/171 (36%), Gaps = 22/171 (12%)
Query: 52 MPKNILLVGPTGVGKT----AISRRLARLAGAPFIKVEVTKFTEIGYV-----GRNVEQI 102
M + + G GVGKT A + +LA +G + V +G V G + ++
Sbjct: 1 MTRIVFFTGKGGVGKTTIAAATAVKLAE-SGKKVLLVSTDPAHSLGDVFDLELGHDPRKV 59
Query: 103 IRDLVDVAINIVRESRR--DEVREQASINAEERILDALVGKTATS--NTREVFRKKLRDG 158
+L + ++ + DEV++ + R L + + E
Sbjct: 60 GPNLDALELDPEKALEEYWDEVKDYLARLLRTRGLGGIYADELATLPGIDEALALLKILE 119
Query: 159 EISDKEIDIEVADTSSDISNFDIPGGASVGILNLSELFSKVMGSGRKKKIR 209
E D+ V DT+ P G ++ +L+L E+ + K + +
Sbjct: 120 YYVSGEYDVIVVDTA--------PTGHTLRLLSLPEVLGWYLEKLFKPRRK 162
>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion..
Length = 165
Score = 32.4 bits (73), Expect = 0.25
Identities = 20/114 (17%), Positives = 39/114 (34%), Gaps = 6/114 (5%)
Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIV 114
IL+ GPTG GKT ++ +LA KV E + I+
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60
Query: 115 RESRRDEVREQASINAEERILDA------LVGKTATSNTREVFRKKLRDGEISD 162
+ D+ ++ ER+ + ++ + ++ GE+ +
Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDE 114
>gnl|CDD|35947 KOG0728, KOG0728, KOG0728, 26S proteasome regulatory complex,
ATPase RPT6 [Posttranslational modification, protein
turnover, chaperones].
Length = 404
Score = 32.3 bits (73), Expect = 0.28
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
PK +LL GP G GKT ++R +A FI+V ++ + Y+G +++R+L +A
Sbjct: 181 PKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQ-KYIGEG-SRMVRELFVMA 236
>gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 32.3 bits (73), Expect = 0.29
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 49 DELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108
P NI++ GPTG GKTA + + VEV + R Q++ +++
Sbjct: 38 RGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLEL--RTPYQVLSKILN 95
Query: 109 VAINI 113
+
Sbjct: 96 KLGKV 100
>gnl|CDD|35961 KOG0742, KOG0742, KOG0742, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 630
Score = 32.3 bits (73), Expect = 0.29
Identities = 35/141 (24%), Positives = 57/141 (40%), Gaps = 20/141 (14%)
Query: 54 KNILLVGPTGVGKTAISRRLARLAG-----------APFIKVEVTKFTEIGYVGRNVEQI 102
+NIL GP G GKT +R LAR +G AP VTK ++ + +
Sbjct: 385 RNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRG 444
Query: 103 IRDLVDVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISD 162
+ +D A + E + + E A+ L+AL+ +T + V
Sbjct: 445 LLLFIDEADAFLCERNKTYMSE-----AQRSALNALLFRTGDQSRDIVLVLATNRPG--- 496
Query: 163 KEIDIEVADTSSDISNFDIPG 183
++D V D ++ F +PG
Sbjct: 497 -DLDSAVNDRIDEVVEFPLPG 516
>gnl|CDD|37239 KOG2028, KOG2028, KOG2028, ATPase related to the helicase subunit
of the Holliday junction resolvase [Replication,
recombination and repair].
Length = 554
Score = 32.0 bits (72), Expect = 0.30
Identities = 24/108 (22%), Positives = 45/108 (41%), Gaps = 18/108 (16%)
Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74
LD Y+ GQ + LR+ + ++P+ ++L GP G GKT ++R +A
Sbjct: 136 TLDDYV-GQSHLVGQDGL-LRSLIEQNRIPS----------MILWGPPGTGKTTLARLIA 183
Query: 75 RLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEV 122
+ +F E+ +RD+ + A N ++R +
Sbjct: 184 STSKKHSY-----RFVELSATNAKTND-VRDIFEQAQNEKSLTKRKTI 225
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 32.0 bits (74), Expect = 0.33
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDL 106
I + G +G GKT + +AR A A ++V + IG GR V + I +L
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV----YVLIGERGREVAEFIEEL 64
>gnl|CDD|37381 KOG2170, KOG2170, KOG2170, ATPase of the AAA+ superfamily [General
function prediction only].
Length = 344
Score = 31.8 bits (72), Expect = 0.37
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 13/64 (20%)
Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLV---GPTGVGKTAISR 71
+L R + GQ AK+ V AL++ W P+ L++ G TG GK ++
Sbjct: 79 DLARALFGQHLAKQLVVNALKSHWANPN----------PRKPLVLSFHGWTGTGKNYVAE 128
Query: 72 RLAR 75
+A
Sbjct: 129 IIAE 132
>gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 31.8 bits (72), Expect = 0.38
Identities = 32/116 (27%), Positives = 54/116 (46%), Gaps = 28/116 (24%)
Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRLAR--- 75
++GQ++A+ A + ++ ++ M + IL+VGP G GKTA++ +AR
Sbjct: 41 LVGQEEAREAAGVIVKM----------IKQGKMAGRGILIVGPPGTGKTALAMGIARELG 90
Query: 76 -------LAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVRE 124
++G+ +EV K TE + Q +R + V I RE EV E
Sbjct: 91 EDVPFVAISGSEIYSLEVKK-TEA------LTQALRRAIGVRIKETREVYEGEVVE 139
>gnl|CDD|35945 KOG0726, KOG0726, KOG0726, 26S proteasome regulatory complex,
ATPase RPT2 [Posttranslational modification, protein
turnover, chaperones].
Length = 440
Score = 31.8 bits (72), Expect = 0.39
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE--IGYVGRNVEQIIRDLVDVA 110
PK ++L G G GKT +++ +A A F++V ++ + +G + V ++ R + A
Sbjct: 219 PKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHA 278
Query: 111 INIV 114
+IV
Sbjct: 279 PSIV 282
>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 31.8 bits (72), Expect = 0.42
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVR 115
I +VGP G GK+ + + LA G V+V + +IGY ++ +++ D + +
Sbjct: 351 IAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDEL--DPDKTVLEELS 408
Query: 116 ESRRDEVREQA 126
E D ++
Sbjct: 409 EGFPDGDEQEV 419
>gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.6 bits (71), Expect = 0.44
Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEI 92
LR + K ILL G GVGKT++ LAR G I++ +++ T++
Sbjct: 1537 LRAMQVGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDL 1582
Score = 30.8 bits (69), Expect = 0.71
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 38 WRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG 93
W +QL +++ + LLVG TG GKT + + LA + ++ TE+
Sbjct: 452 WLLEQLLWNIQ---NNEPTLLVGETGTGKTTMIQYLALKLHFKLTVINKSQQTEMS 504
Score = 29.3 bits (65), Expect = 2.0
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG-YVG 96
+L+ GPT GKT++ LAR G F+++ + T++ Y+G
Sbjct: 891 LLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIG 932
Score = 28.9 bits (64), Expect = 2.7
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGA 79
++LVG TGVGKT++ R LA + G
Sbjct: 1853 LILVGDTGVGKTSLLRFLASIFGQ 1876
>gnl|CDD|133262 cd01853, Toc34_like, Toc34-like (Translocon at the Outer-envelope
membrane of Chloroplasts). This family contains
several Toc proteins, including Toc34, Toc33, Toc120,
Toc159, Toc86, Toc125, and Toc90. The Toc complex at
the outer envelope membrane of chloroplasts is a
molecular machine of ~500 kDa that contains a single
Toc159 protein, four Toc75 molecules, and four or five
copies of Toc34. Toc64 and Toc12 are associated with
the translocon, but do not appear to be part of the
core complex. The Toc translocon initiates the import
of nuclear-encoded preproteins from the cytosol into
the organelle. Toc34 and Toc159 are both GTPases,
while Toc75 is a beta-barrel integral membrane protein.
Toc159 is equally distributed between a soluble
cytoplasmic form and a membrane-inserted form,
suggesting that assembly of the Toc complex is dynamic.
Toc34 and Toc75 act sequentially to mediate docking
and insertion of Toc159 resulting in assembly of the
functional translocon.
Length = 249
Score = 31.5 bits (72), Expect = 0.48
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 42 QLPADLRDELMPK-NILLVGPTGVGKTAI 69
+L A ++EL IL++G TGVGK++
Sbjct: 19 ELEAKGKEELDFSLTILVLGKTGVGKSST 47
>gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear
protein involved oxidative stress response [Nucleotide
transport and metabolism].
Length = 176
Score = 31.4 bits (71), Expect = 0.55
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV 84
NIL+ G G GK+ ++ RLA G +I++
Sbjct: 9 NILVTGTPGTGKSTLAERLAEKTGLEYIEI 38
>gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 31.4 bits (72), Expect = 0.56
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 53 PKNILLVGPTGVGKTAISRRLARL 76
P ILLVG G GKT +LA
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAY 24
>gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis)
represents a protein family whose members are broadly
conserved in bacteria and have been shown to be
essential to the growth of E. coli and B. subtilis.
Proteins of the YjeQ family contain all sequence motifs
typical of the vast class of P-loop-containing GTPases,
but show a circular permutation, with a G4-G1-G3 pattern
of motifs as opposed to the regular G1-G3-G4 pattern
seen in most GTPases. All YjeQ family proteins display a
unique domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain. This domain architecture suggests a role for
YjeQ as a regulator of translation..
Length = 287
Score = 31.3 bits (71), Expect = 0.57
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLA 74
+LR+ L K +LVG +GVGK+ + L
Sbjct: 153 DELREYLKGKTSVLVGQSGVGKSTLINALL 182
>gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor..
Length = 147
Score = 31.3 bits (71), Expect = 0.58
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 9/68 (13%)
Query: 60 GPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQI--IRDLVDVAI------ 111
GP G GK+ +++ LA+ G P++ + E+G + V I +R +D
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLDTGGIRTEEVGKLASEVAAIPEVRKALDERQRELAKK 65
Query: 112 -NIVRESR 118
IV E R
Sbjct: 66 PGIVLEGR 73
>gnl|CDD|29833 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the phosphorylation
state of the phosphocarrier protein HPr and regulates
the utilization of carbon sources by gram-positive
bacteria. It catalyzes both the ATP-dependent
phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter reaction
uses inorganic phosphate as substrate and produces
pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK)
and the C-terminal catalytic domain of HprK/P are
structurally similar with conserved active site residues
suggesting these two phosphotransferases have related
functions. The HprK/P N-terminal domain is structurally
similar to the N-terminal domains of the MurE and MurF
amino acid ligases..
Length = 149
Score = 31.0 bits (70), Expect = 0.60
Identities = 22/127 (17%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG--YVGRNVEQIIRDLVDV---- 109
+L+ GP+G+GK+ ++ L + G + + G VGR E ++ L+++
Sbjct: 17 VLITGPSGIGKSELALELIK-RGHRLVADDRVVVKREGGRLVGRAPE-ALKGLIEIRGLG 74
Query: 110 AINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDIEV 169
I++ R + VR++ I+ + + K E K++ ++ + +
Sbjct: 75 IIDVPRLYGIEAVRDRKVIDLVIELEEWEEEKNFDRLGLEEEYKRILGVKVPLLRLPVSP 134
Query: 170 ADTSSDI 176
+ +
Sbjct: 135 GRNLAVL 141
>gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 103
Score = 31.0 bits (71), Expect = 0.65
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKV 84
K L+V TG GKT + +L KV
Sbjct: 19 KRGLIVMATGSGKTLTAAKLIARLLKGKKKV 49
>gnl|CDD|36760 KOG1547, KOG1547, KOG1547, Septin CDC10 and related P-loop GTPases
[Cell cycle control, cell division, chromosome
partitioning, Signal transduction mechanisms,
Cytoskeleton].
Length = 336
Score = 30.7 bits (69), Expect = 0.79
Identities = 22/109 (20%), Positives = 44/109 (40%), Gaps = 24/109 (22%)
Query: 55 NILLVGPTGVGKTAI-----SRRLARLAGAPFIKVEVTKFTEIGYVGRNVE----QIIRD 105
NI++VG +G+GK+ + ++ + + + K TEI + +E ++
Sbjct: 48 NIMVVGQSGLGKSTLINTLFKSHVSDSSSSDNSAEPIPKTTEIKSITHVIEEKGVKLKLT 107
Query: 106 LVDVA---------------INIVRESRRDEVREQASINAEERILDALV 139
++D + E +RE+ +I E+RI D V
Sbjct: 108 VIDTPGFGDQINNDNCWEPIEKYINEQYEQYLREELNIAREKRIPDTRV 156
>gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family
within the Ras superfamily. There are at least 60 Rab
genes in the human genome, and a number of Rab GTPases
are conserved from yeast to humans. Rab GTPases are
small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways.
In the GTP-bound form, Rab GTPases recruit specific
sets of effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Since crystal structures often lack
C-terminal residues, the lipid modification site is not
available for annotation in many of the CDs in the
hierarchy, but is included where possible.
Length = 159
Score = 30.5 bits (70), Expect = 0.86
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 56 ILLVGPTGVGKTAISRRL 73
I+L+G +GVGKT++ R
Sbjct: 3 IVLIGDSGVGKTSLLLRF 20
>gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 122
Score = 30.4 bits (69), Expect = 1.1
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG 93
+L+VGP GKT + R+L +V V K + G
Sbjct: 3 VLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHG 40
>gnl|CDD|32436 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 30.1 bits (68), Expect = 1.1
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 9/55 (16%)
Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
IGQ+ K + I ++ A R E ++LL GP G+GKT ++ +A
Sbjct: 29 IGQEKVKEQLQIFIK--------AAKKRGE-ALDHVLLFGPPGLGKTTLAHIIAN 74
>gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 30.2 bits (68), Expect = 1.2
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 38 WRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
WRR +R P IL+ G +GVGK+ I+ LAR
Sbjct: 80 WRR------IRKMKRPLIILIGGASGVGKSTIAGELAR 111
>gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 30.2 bits (69), Expect = 1.2
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLA 74
+L+ L K +L G +GVGK+ + L
Sbjct: 27 EELKPLLKGKTSVLAGQSGVGKSTLLNALL 56
>gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 29.9 bits (67), Expect = 1.3
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 41 QQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74
+L + L K +L+G +GVGK+ + L
Sbjct: 152 GDGLEELAELLAGKITVLLGQSGVGKSTLINALL 185
>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
factor (pNORF1) [RNA processing and modification].
Length = 935
Score = 30.0 bits (67), Expect = 1.3
Identities = 34/173 (19%), Positives = 63/173 (36%), Gaps = 29/173 (16%)
Query: 57 LLVGPTGVGKT----AISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAIN 112
L+ GP G GKT I LAR P + + V+Q+ + +
Sbjct: 429 LIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIA--------VDQLAEKIHKTGLK 480
Query: 113 IVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDIEVADT 172
+VR + RE + L + +++ + K GE+S +
Sbjct: 481 VVRLCAKS--REDIESDVSFLSLHEQLRNMDKPELQKLLKLKDEGGELSSSD-------- 530
Query: 173 SSDISNFDIPGGASVGILNLSE-LFSKVMGSGRKKKIRMSVQKCYPELMRDES 224
+ + A +LN ++ + +G+G + R+S K L+ DE+
Sbjct: 531 --EKKYRKLKRAAEKELLNQADVICCTCVGAGDR---RLSKFKFRTVLI-DEA 577
>gnl|CDD|32386 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 29.9 bits (67), Expect = 1.3
Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 14/96 (14%)
Query: 3 LTFNFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPA------DLRDEL----- 51
L F +++ ++R + ++ + R + +L LR +
Sbjct: 103 LEKPFDLDRLLAIVERALELRELQRENRRSLKRAKSLGGELVGESPAMQQLRRLIAKVAP 162
Query: 52 MPKNILLVGPTGVGKTAISR---RLARLAGAPFIKV 84
++L+ G +G GK ++R + + A PFI V
Sbjct: 163 SDASVLITGESGTGKELVARAIHQASPRAKGPFIAV 198
>gnl|CDD|73174 COG0470, HolB, ATPase involved in DNA replication [DNA
replication, recombination, and repair].
Length = 325
Score = 29.9 bits (66), Expect = 1.3
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 40 RQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
++ L L +P +L GP GVGKT + LA+
Sbjct: 11 KRLLVQALESGRLPHALLFYGPPGVGKTTAALALAK 46
>gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 29.9 bits (68), Expect = 1.3
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 55 NILLVGPTGVGKTAISRRLARLA 77
N+LL+GP GVGKT ++ L A
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQA 71
>gnl|CDD|30990 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 29.9 bits (67), Expect = 1.4
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
+L+ G G GK+ ++R LA L GA ++ +V
Sbjct: 4 VLVGGLPGSGKSTLARGLAELLGAIRLRSDV 34
>gnl|CDD|35955 KOG0736, KOG0736, KOG0736, Peroxisome assembly factor 2 containing
the AAA+-type ATPase domain [Posttranslational
modification, protein turnover, chaperones].
Length = 953
Score = 30.0 bits (67), Expect = 1.5
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT 90
+LL GP G GKT + R +A G ++V+ +
Sbjct: 434 VLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELV 468
>gnl|CDD|132912 cd07041, STAS_RsbR_RsbS_like, Sulphate Transporter and Anti-Sigma
factor antagonist domain of the "stressosome" complex
proteins RsbS and RsbR, regulators of the bacterial
stress activated alternative sigma factor sigma-B by
phosphorylation. The STAS (Sulphate Transporter and
Anti-Sigma factor antagonist) domain of proteins related
to RsbS and RsbR which are part of the "stressosome"
complex that plays an important role in the regulation
of the bacterial stress activated alternative sigma
factor sigma-B. During stress conditions RsbS and RsbR
are phosphorylated which leads to the release of RsbT,
an activator of of the RsbU phosphatase, which in turn
activates RsbV which leads to the release and activation
of sigma factor B. RsbS is a single domain protein (STAS
domain), while RsbR-like proteins have a well-conserved
C-terminal STATS domain and a variable N-terminal
domain. The STAS domain is also found in the C- terminal
region of sulphate transporters and anti-anti-sigma
factors.
Length = 109
Score = 29.7 bits (68), Expect = 1.6
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 381 VGDIGARRLQTVMERVLEDISFSASDLQEKTVVID 415
+GD+ R + + ER+LE I S + + V+ID
Sbjct: 17 IGDLDDERAEQLQERLLEAI----SRRRARGVIID 47
>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.6 bits (66), Expect = 1.6
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 55 NILLVGPTGVGKTAISRRLARL 76
N L++GP VGKT + R +ARL
Sbjct: 139 NTLIIGPPQVGKTTLLRDIARL 160
>gnl|CDD|37180 KOG1969, KOG1969, KOG1969, DNA replication checkpoint protein
CHL12/CTF18 [Energy production and conversion,
Replication, recombination and repair].
Length = 877
Score = 29.6 bits (66), Expect = 1.6
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 38 WRRQQLPADLRDELMP--KNILLVGPTGVGKTAISRRLARLAG 78
++ L +L P K +LL GP G+GKT ++ +A+ AG
Sbjct: 309 TEKEVLDMELDPSKRPPKKILLLCGPPGLGKTTLAHVIAKQAG 351
>gnl|CDD|30631 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 29.8 bits (67), Expect = 1.7
Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 20/110 (18%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFI----------------KVEVTKFTEIGYV 95
I + GP G GK+ +++ LA G ++ V++ + +
Sbjct: 3 AAIIIAIDGPAGSGKSTVAKILAEKLGFHYLDTGAMYRAVALAALKHGVDLDDEDALVAL 62
Query: 96 GRNVEQIIRDLVDVAIN---IVRESRRDEVREQAS-INAEERILDALVGK 141
+ ++ + V +N + E R +EV AS + A + +ALV
Sbjct: 63 AKELDISFVNDDRVFLNGEDVSEEIRTEEVGNAASKVAAIPEVREALVKL 112
>gnl|CDD|34269 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 29.6 bits (66), Expect = 1.8
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 26/86 (30%)
Query: 25 DAKRAVAIALRNRWRRQQLPADLRDELMPKN--------------------ILLVGPTGV 64
D R AIA R R+Q L+ + +N ILL GPTG
Sbjct: 160 DLSRYNAIASRFAEEREQTLDFLKSGIATRNPHFNRMIEQIERVAIRSRAPILLNGPTGA 219
Query: 65 GKTAISRRLARLAGA------PFIKV 84
GK+ ++RR+ L A F++V
Sbjct: 220 GKSFLARRIYELKQARHQFSGAFVEV 245
>gnl|CDD|147726 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 29.6 bits (67), Expect = 1.9
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAP 80
++L G G GKT + ++LA L
Sbjct: 3 VILQGEAGSGKTTLLQKLALLWAQG 27
>gnl|CDD|112109 pfam03279, Lip_A_acyltrans, Bacterial lipid A biosynthesis
acyltransferase.
Length = 295
Score = 29.6 bits (67), Expect = 1.9
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 9/50 (18%)
Query: 200 MGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRDSIQMVENYGIVFL 249
G R+K R ++ C+PE+ E +++ID Q + ++G+ L
Sbjct: 48 FGKRRRKIARKNLALCFPEMSEAEREKIID---------QSLASFGMAIL 88
>gnl|CDD|38288 KOG3078, KOG3078, KOG3078, Adenylate kinase [Nucleotide transport
and metabolism].
Length = 235
Score = 29.5 bits (66), Expect = 2.0
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 6/57 (10%)
Query: 43 LPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIG 93
P DE +L+G G GK + RL + G I E+ TE+G
Sbjct: 5 APGFDEDEKKGVRAVLLGAPGSGKGTQAPRLTKNFGVIHISTGDLLRDEIASGTELG 61
>gnl|CDD|146942 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears
to be involved in plant resistance to bacteria.
Length = 200
Score = 29.5 bits (67), Expect = 2.0
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 54 KNILLVGPTGVGKTA 68
I+LVG TG GK+A
Sbjct: 1 LRIVLVGKTGNGKSA 15
>gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 167
Score = 29.1 bits (66), Expect = 2.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 51 LMPKNILLVGPTGVGKTAI 69
L K++L+ PTG GKT
Sbjct: 12 LEGKDVLVQAPTGSGKTLA 30
>gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.9 bits (64), Expect = 2.6
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 27 KRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
A LR ++ + L A +++ + ++V PTG GKT ++ + +
Sbjct: 30 IVAFEFELRP-YQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLVP 88
Query: 87 TK 88
TK
Sbjct: 89 TK 90
>gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 29.1 bits (66), Expect = 2.7
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 56 ILLVGPTGVGKTAISRRLAR 75
I L GP G GK+ +++ LAR
Sbjct: 1 IWLYGPPGCGKSTLAKYLAR 20
>gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.1 bits (65), Expect = 2.7
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFI 82
IL++GP G GK+ ++++LA+ G P +
Sbjct: 1 MRILILGPPGAGKSTLAKKLAKKLGLPHL 29
>gnl|CDD|33076 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 29.1 bits (65), Expect = 2.8
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 60 GPTGVGKTAISRRLARLAGAPFI 82
G +G GK+ + LA GA FI
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFI 24
>gnl|CDD|32119 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 28.7 bits (64), Expect = 2.9
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 54 KNILLVGPTGVGKTAISRRLARLA 77
I + G GVGKT + + L L
Sbjct: 1 MLIAITGTPGVGKTTVCKLLRELG 24
>gnl|CDD|73180 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines..
Length = 137
Score = 29.0 bits (65), Expect = 2.9
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 56 ILLVGPTGVGKTAISRRL 73
I+L GP+GVGK+ + +RL
Sbjct: 2 IVLSGPSGVGKSTLLKRL 19
>gnl|CDD|147593 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyses the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalysed 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 = 234
Score = 29.0 bits (66), Expect = 2.9
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 16 LDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
LD YI GQ+ K + I + A R E + ++LL GP G+GKT ++ +A
Sbjct: 23 LDEYI-GQEKVKENLKIFIE--------AAKKRGEAL-DHVLLYGPPGLGKTTLANIIAN 72
Query: 76 LAGAPF 81
G
Sbjct: 73 EMGVNI 78
>gnl|CDD|31198 COG0857, Pta, BioD-like N-terminal domain of phosphotransacetylase
[General function prediction only].
Length = 354
Score = 28.7 bits (64), Expect = 3.1
Identities = 31/141 (21%), Positives = 51/141 (36%), Gaps = 19/141 (13%)
Query: 52 MPKNILLVGP-TGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
M + +LL+ TGVGKT+IS L R +KV K I A
Sbjct: 1 MSRTLLLIPTETGVGKTSISLGLLRALEQKGLKVAYFK------------PIGTRTGKDA 48
Query: 111 INIVRESRRDEVREQASIN-AEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDIEV 169
++ E D +S+ AE +L +T + + L + K+ D+ V
Sbjct: 49 DDLTEE---DIRATSSSLTYAEPLVLSFAEVLLSTGQDDVLLEEILANYAELAKDADVVV 105
Query: 170 ADTSSDISNFDIPGGASVGIL 190
+ D+ + P +
Sbjct: 106 VE--GDVPTREGPYALDLNYE 124
>gnl|CDD|133313 cd04113, Rab4, Rab4 subfamily. Rab4 has been implicated in
numerous functions within the cell. It helps regulate
endocytosis through the sorting, recycling, and
degradation of early endosomes. Mammalian Rab4 is
involved in the regulation of many surface proteins
including G-protein-coupled receptors, transferrin
receptor, integrins, and surfactant protein A.
Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 161
Score = 28.8 bits (65), Expect = 3.2
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 56 ILLVGPTGVGKTAISRRL 73
+++G +G GK+ + R
Sbjct: 3 FIIIGSSGTGKSCLLHRF 20
>gnl|CDD|35305 KOG0082, KOG0082, KOG0082, G-protein alpha subunit (small G protein
superfamily) [Cell cycle control, cell division,
chromosome partitioning, Signal transduction
mechanisms].
Length = 354
Score = 28.6 bits (64), Expect = 3.4
Identities = 21/101 (20%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 35 RNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGY 94
R++ +QL + + E +LL+G GK+ I +++ L G F + E+ ++ + Y
Sbjct: 15 RSKEIDKQLKKEKKKEKKIIKLLLLGAGESGKSTIVKQMKILHGDGFSEEELLEYRPVIY 74
Query: 95 VGRNVEQIIRDLVD----VAINIVRESRRDEVREQASINAE 131
N+ Q ++ L+ + IN+ R ++ ++ +
Sbjct: 75 --SNIIQSLKALLRAMETLGINLDDPERENDAQKLTLLADA 113
>gnl|CDD|31748 COG1560, HtrB, Lauroyl/myristoyl acyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 308
Score = 28.7 bits (64), Expect = 3.5
Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 10/56 (17%)
Query: 195 LFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRDSIQMVENYGIVFLD 250
L +++ RK R ++ C+PE E ++++ + + G L+
Sbjct: 46 LAGRLLKRRRKI-ARRNLALCFPEKSEAEREKIVK---------ESFASMGRALLE 91
>gnl|CDD|35958 KOG0739, KOG0739, KOG0739, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 439
Score = 28.4 bits (63), Expect = 3.7
Identities = 33/118 (27%), Positives = 52/118 (44%), Gaps = 18/118 (15%)
Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHILFIASGAFH 305
I+F+DE D + S N SR ++ + L ++G + D +L + +
Sbjct: 228 IIFIDEIDSLCGSRSENESEASRR-IKTEFLVQMQGVGN-------DNDGVLVLGA---- 275
Query: 306 VSRPADLLPEIQGRFPVRVHLKSLNKSD----FRLILTDTESNLILQ-YKEL-MKTEG 357
+ P L I+ RF R+++ F+L L DT L Q +KEL KTEG
Sbjct: 276 TNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEG 333
Score = 28.0 bits (62), Expect = 4.6
Identities = 16/57 (28%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
+ ILL GP G GK+ +++ +A A + F V + ++G + E+++++L ++A
Sbjct: 167 RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS-KWMGES-EKLVKNLFEMA 221
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G
in the GTP form binds to the ribosome, primarily
through the interaction of its EF-Tu-like domain with
the 50S subunit. The binding of EF-G to the ribosome
in this manner stimulates the GTPase activity of EF-G.
On GTP hydrolysis, EF-G undergoes a conformational
change that forces its arm deeper into the A site on
the 30S subunit. To accommodate this domain, the
peptidyl-tRNA in the A site moves to the P site,
carrying the mRNA and the deacylated tRNA with it. The
ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation
of EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains
only bacterial members.
Length = 268
Score = 28.7 bits (65), Expect = 3.7
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 55 NILLVGPTGVGKTAISRRLARLAGA 79
NI LVG +G GKT ++ L GA
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGA 25
>gnl|CDD|32539 COG2403, COG2403, Predicted GTPase [General function prediction
only].
Length = 449
Score = 28.4 bits (63), Expect = 3.9
Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 3/89 (3%)
Query: 62 TGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDE 121
TGVGK+A+SR +ARL +V V + I Y G +E + L + ++ R + DE
Sbjct: 136 TGVGKSAVSRYVARLLRERGYRVCVVRHPMI-YRGDRIEITVERLAKLE-DLDRHAATDE 193
Query: 122 VREQASINAEERILDALVGKTATSNTREV 150
RE + L G + +E
Sbjct: 194 ERE-EYESYIPTGGGVLAGVDYGTVLKEG 221
>gnl|CDD|33404 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 28.4 bits (63), Expect = 4.0
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 55 NILLVGPTGVGKTAISRRLARL---AGAPFIKV 84
+L+ G TG GK ++R + +L PF+K+
Sbjct: 248 TVLIRGETGTGKELVARAIHQLSPRRDKPFVKL 280
>gnl|CDD|133261 cd01852, AIG1, AIG1 (avrRpt2-induced gene 1). This represents
Arabidoposis protein AIG1 that appears to be involved
in plant resistance to bacteria. The Arabidopsis
disease resistance gene RPS2 is involved in recognition
of bacterial pathogens carrying the avirulence gene
avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent
induction early after infection with Pseudomonas
syringae carrying avrRpt2. This subfamily also includes
IAN-4 protein, which has GTP-binding activity and
shares sequence homology with a novel family of
putative GTP-binding proteins: the immuno-associated
nucleotide (IAN) family. The evolutionary conservation
of the IAN family provides a unique example of a plant
pathogen response gene conserved in animals. The
IAN/IMAP subfamily has been proposed to regulate
apoptosis in vertebrates and angiosperm plants,
particularly in relation to cancer, diabetes, and
infections. The human IAN genes were renamed GIMAP
(GTPase of the immunity associated proteins).
Length = 196
Score = 28.3 bits (64), Expect = 4.1
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 54 KNILLVGPTGVGKTA 68
++LVG TG GK+A
Sbjct: 1 LRLVLVGKTGAGKSA 15
>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
functions primarily to fill DNA gaps that arise during
DNA repair, recombination and replication.
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human
polymerase beta (class x), E. coli UmuC/DinB and
eukaryotic RAP 30/Xeroderma pigmentosum variant (class
Y). Family A polymerase are found primarily in
organisms related to prokaryotes and include
prokaryotic DNA polymerase I ,mitochondrial polymerase
delta, and several bacteriphage polymerases including
those from odd-numbered phage (T3, T5, and T7).
Prokaryotic Pol Is have two functional domains located
on the same polypeptide; a 5'-3' polymerase and 5'-3'
exonuclease. Pol I uses its 5' nuclease activity to
remove the ribonucleotide portion of newly synthesized
Okazaki fragments and DNA polymerase activity to fill
in the resulting gap. A combination of phylogenomic and
signature sequence-based (or phonetic) approaches is
used to understand the evolutionary relationships among
bacteria. DNA polymerase I is one of the conserved
proteins that is used to search for protein signatures.
The structure of these polymerases resembles in overall
morphology a cupped human right hand, with fingers
(which bind an incoming nucleotide and interact with
the single-stranded template), palm (which harbors the
catalytic amino acid residues and also binds an
incoming dNTP) and thumb (which binds double-stranded
DNA) subdomains.
Length = 429
Score = 28.2 bits (63), Expect = 4.5
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 25 DAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVG---KTAISRRLARLAGAPF 81
+ ++A + + RR+ L +L++ P + G +T + + GAP+
Sbjct: 2 NQEKAAKLYAQLAGRREDLENELQEVFPPWYV----SDGFVPKKRTTNNSVRGYVKGAPY 57
Query: 82 IKVEVTKF 89
K+++ F
Sbjct: 58 TKIKLVTF 65
>gnl|CDD|35279 KOG0056, KOG0056, KOG0056, Heavy metal exporter HMT1, ABC
superfamily [Inorganic ion transport and metabolism].
Length = 790
Score = 28.1 bits (62), Expect = 4.6
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 46 DLRDELMP-KNILLVGPTGVGKTAISRRLARL 76
D+ + P K + LVGP+G GK+ I R L R
Sbjct: 556 DISFTVQPGKTVALVGPSGAGKSTIMRLLFRF 587
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 28.1 bits (63), Expect = 4.7
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
P+ +LLVG G GK+ ++ +A P ++++V K G VG + E +R ++ +A
Sbjct: 259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFG-GIVGES-ESRMRQMIRIA 314
>gnl|CDD|33684 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
mechanisms].
Length = 205
Score = 28.1 bits (62), Expect = 4.7
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91
+LL G + GK++I+ LA P++ + + F E
Sbjct: 26 VLLNGGSSAGKSSIALAFQDLAAEPWMHIGIDLFWE 61
>gnl|CDD|35575 KOG0354, KOG0354, KOG0354, DEAD-box like helicase [General
function prediction only].
Length = 746
Score = 28.0 bits (62), Expect = 4.8
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRD---EL----MPKNILLVGPTGVGKTAISRR 72
I A ++ + RW +LR+ EL + KN ++ PTG GKT I+
Sbjct: 37 IDQNNSASHSLDESAAQRWIYPT-NLELRNYQEELVQPALGKNTIIALPTGSGKTFIAAV 95
Query: 73 LA 74
+
Sbjct: 96 IM 97
>gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 28.2 bits (63), Expect = 4.9
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 50 ELMPKNIL-LVGPTGVGKTAISRRLARL 76
+L L LVG +G GK+ ++R LA L
Sbjct: 313 DLREGETLGLVGESGSGKSTLARILAGL 340
>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 28.0 bits (62), Expect = 5.3
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 32 IALRNRWRRQQLPADLRD----ELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVT 87
+ +++ LR E P N+LL+G TG GK+++ L + KV V
Sbjct: 14 LLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVG 73
Query: 88 K 88
Sbjct: 74 T 74
>gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 27.9 bits (62), Expect = 5.3
Identities = 12/54 (22%), Positives = 23/54 (42%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRD 105
I++ G G GKT + L IKV +T+ +G + +++ +
Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTREPGGTPIGEKIRELLLN 55
>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, 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 = 27.8 bits (62), Expect = 5.5
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 54 KNILLVGPTGVGKTAISRRLARL 76
+L+ GP+G GK+++ R LA L
Sbjct: 28 DRLLITGPSGTGKSSLFRALAGL 50
>gnl|CDD|153328 cd07644, I-BAR_IMD_BAIAP2L2, Inverse (I)-BAR, also known as the
IRSp53/MIM homology Domain (IMD), of Brain-specific
Angiogenesis Inhibitor 1-Associated Protein 2-Like 2.
The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs
(I-BAR) domain, is a dimerization and lipid-binding
module that bends membranes and induces membrane
protrusions. This group is composed of uncharacterized
proteins known as BAIAP2L2 (Brain-specific Angiogenesis
Inhibitor 1-Associated Protein 2-Like 2). They contain
an N-terminal IMD, an SH3 domain, and a WASP homology 2
(WH2) actin-binding motif at the C-terminus. The related
proteins, BAIAP2L1 and IRSp53, function as regulators of
membrane dynamics and the actin cytoskeleton. The IMD
domain binds and bundles actin filaments, binds
membranes and produces membrane protrusions, and
interacts with the small GTPase Rac.
Length = 215
Score = 28.0 bits (62), Expect = 5.5
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 369 ALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVIDAEYV 419
AL++ A S + IG + LQ++ + L +I S+ Q + + D E V
Sbjct: 38 ALSEAAEVYFSAIAKIGEQALQSLTSQSLGEILIQMSETQ-RKLSADLEVV 87
>gnl|CDD|35283 KOG0060, KOG0060, KOG0060, Long-chain acyl-CoA transporter, ABC
superfamily (involved in peroxisome organization and
biogenesis) [Lipid transport and metabolism, General
function prediction only].
Length = 659
Score = 28.0 bits (62), Expect = 5.8
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 54 KNILLVGPTGVGKTAISRRLARL 76
+N+L+ GP+G GKT++ R L L
Sbjct: 462 QNLLITGPSGCGKTSLLRVLGGL 484
>gnl|CDD|30481 COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism].
Length = 223
Score = 27.9 bits (62), Expect = 6.1
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 52 MPKNILLVGP-TGVGKTAISRRLARLAGAPFIKVEVTK 88
M K + G TGVGKT +S LA+ V K
Sbjct: 1 MMKRFFVTGTDTGVGKTVVSAALAQALKQQGYSVAGYK 38
>gnl|CDD|31674 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 27.9 bits (62), Expect = 6.4
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 9/58 (15%)
Query: 10 REIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKT 67
+ LDR + + A R+ AL + R P + + L G G GKT
Sbjct: 31 PAAAAALDR-LYDELVAPRSARKALGWLFGRDHGP--------VRGLYLWGGVGRGKT 79
>gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily
includes classical N-Ras, H-Ras, and K-Ras, as well as
R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1,
RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins
regulate cell growth, proliferation and
differentiation. Ras is activated by guanine
nucleotide exchange factors (GEFs) that release GDP and
allow GTP binding. Many RasGEFs have been identified.
These are sequestered in the cytosol until activation
by growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active GTP-bound Ras interacts with several effector
proteins: among the best characterized are the Raf
kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs
and NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not
available for annotation.
Length = 160
Score = 27.9 bits (63), Expect = 6.5
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 55 NILLVGPTGVGKTAISRRL 73
++++G GVGK+AI+ +
Sbjct: 1 KVVVLGAGGVGKSAITIQF 19
>gnl|CDD|31308 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 27.5 bits (61), Expect = 6.8
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 54 KNILLVGPTGVGKTAIS 70
KN L+V PTG+GKT I+
Sbjct: 30 KNTLVVLPTGLGKTFIA 46
>gnl|CDD|32641 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 27.7 bits (61), Expect = 7.1
Identities = 25/78 (32%), Positives = 30/78 (38%), Gaps = 21/78 (26%)
Query: 56 ILLVGPTGVGKTAISRRLAR-------LAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108
L GP GVGKT I+R LA+ P K K G L+D
Sbjct: 41 YLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGS-----------LID 89
Query: 109 VAINIVRESRR--DEVRE 124
V I I S D++RE
Sbjct: 90 V-IEIDAASNTGVDDIRE 106
>gnl|CDD|29278 cd00227, CPT, Chloramphenicol (Cm) phosphotransferase (CPT).
Cm-inactivating enzyme; modifies the primary (C-3)
hydroxyl of the antibiotic. Related structurally to
shikimate kinase II..
Length = 175
Score = 27.6 bits (61), Expect = 7.2
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91
I+L G + GK++I+R L + P++ V F E
Sbjct: 5 IILNGGSSAGKSSIARALQSVLAEPWLHFGVDSFIE 40
>gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 27.6 bits (61), Expect = 7.5
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 6/78 (7%)
Query: 7 FSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGK 66
S + + + + +D + + W + A +M +VGP GK
Sbjct: 33 LSVARVRTTYHQLVEVPEDRSEP-LEEIADTWESKSESAGKVGVVM-----VVGPVDSGK 86
Query: 67 TAISRRLARLAGAPFIKV 84
+ ++ LA A KV
Sbjct: 87 STLTTYLANKLLARGRKV 104
>gnl|CDD|33622 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 27.6 bits (61), Expect = 7.8
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 52 MPKNILLVGPTGVGKTAISRRLARL---AGAPFIKV 84
+L++G +G GK +R + L A PFI +
Sbjct: 267 TDSTVLILGESGTGKELFARAIHNLSPRANGPFIAI 302
>gnl|CDD|31434 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 27.6 bits (61), Expect = 7.9
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 16/76 (21%)
Query: 11 EIVSELDRYII----GQQDAKRAVAIAL-----RNRWRRQQLPADLRDELMPKNILLVGP 61
+I L + I G +D K+A+ + L +N ++ D+ +ILLVG
Sbjct: 275 DIYDILIKSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDI-------HILLVGD 327
Query: 62 TGVGKTAISRRLARLA 77
G K+ + + +A+LA
Sbjct: 328 PGTAKSQLLKYVAKLA 343
>gnl|CDD|144183 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 27.5 bits (62), Expect = 7.9
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 12/63 (19%)
Query: 20 IIGQQDAKRAVAIAL-----RNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74
I G +D K+A+ + L +N +L D+ N+LLVG G K+ + + +A
Sbjct: 26 IYGHEDVKKAILLQLFGGVKKNLPDGTRLRGDI-------NVLLVGDPGTAKSQLLKYVA 78
Query: 75 RLA 77
+LA
Sbjct: 79 KLA 81
>gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 27.3 bits (60), Expect = 8.2
Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 11/87 (12%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVE-----QIIRDLVDV- 109
+L+ G +G+GK+A+ + + KF + RN+ Q RDL+
Sbjct: 27 VLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQF---ERNIPLSPLVQAFRDLMGQL 83
Query: 110 --AINIVRESRRDEVREQASINAEERI 134
+ S R + N + I
Sbjct: 84 LSESDTRILSWRARLLAALGENGQVII 110
>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
nucleotide-binding domain; ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters
are a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins..
Length = 157
Score = 27.2 bits (60), Expect = 8.3
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
+ LVGP G GK+ + R +A L ++ +
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILI 58
>gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 27.3 bits (60), Expect = 8.5
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 52 MPKNILLVGPTGVGKT----AISRRLAR 75
+N++L+GP GVGKT AI L +
Sbjct: 104 RGENLVLLGPPGVGKTHLAIAIGNELLK 131
>gnl|CDD|30191 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA..
Length = 193
Score = 27.1 bits (60), Expect = 8.6
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82
I++ G G GK+ +++ LA G +
Sbjct: 2 IVVEGNIGAGKSTLAKELAEHLGYEVV 28
>gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 27.1 bits (60), Expect = 8.7
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82
I + G G GKT ++R LA G +
Sbjct: 3 ITISGLPGSGKTTVARELAEHLGLKLV 29
>gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 27.2 bits (60), Expect = 9.3
Identities = 26/119 (21%), Positives = 43/119 (36%), Gaps = 23/119 (19%)
Query: 56 ILLVGPTGVGKTAISRRLARLA----GAPFIKVEVTKFTE--------IGYVGRNVE-QI 102
+LL+GP G GK+ + + L L G + T + +G V +N + Q+
Sbjct: 33 VLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDTSSEKSLLELRQKVGLVFQNPDDQL 92
Query: 103 IRDLV--DVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGE 159
V +VA + E EER+ +AL + L G+
Sbjct: 93 FGPTVEDEVAFGLENLGLPRE-------EIEERVAEALE-LVGLEELLDRPPFNLSGGQ 143
>gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing
and modification].
Length = 674
Score = 27.2 bits (60), Expect = 9.6
Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 6/34 (17%)
Query: 40 RQQLP-ADLRDELMP-----KNILLVGPTGVGKT 67
R+ LP RD+++ + ++++G TG GK+
Sbjct: 47 RESLPIYKYRDQILYAVEDNQVLIVIGETGSGKS 80
>gnl|CDD|31564 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 26.9 bits (59), Expect = 9.9
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 50 ELMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82
+L P IL++GP VGKT + + L + I
Sbjct: 34 DLRPFIILILGPRQVGKTTLLKLLIKGLLEEII 66
>gnl|CDD|30199 cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in
the Benson-Calvin cycle in chloroplasts or
photosynthetic prokaryotes. This enzyme catalyzes the
phosphorylation of D-ribulose 5-phosphate to form
D-ribulose 1, 5-biphosphate, using ATP and NADPH
produced by the primary reactions of photosynthesis..
Length = 273
Score = 27.1 bits (60), Expect = 9.9
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 58 LVGPTGVGKTAISRRLARLAGAPFIKV 84
+ G +G GK+ RRL L G+ + V
Sbjct: 4 VAGDSGCGKSTFLRRLTSLFGSDLVTV 30
>gnl|CDD|36646 KOG1433, KOG1433, KOG1433, DNA repair protein RAD51/RHP55
[Replication, recombination and repair].
Length = 326
Score = 26.9 bits (59), Expect = 10.0
Identities = 13/28 (46%), Positives = 14/28 (50%)
Query: 57 LLVGPTGVGKTAISRRLARLAGAPFIKV 84
LVGP G GKT + LA G KV
Sbjct: 115 ELVGPPGSGKTQLCHTLAVTCGGGEGKV 142
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.137 0.376
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,092,510
Number of extensions: 276548
Number of successful extensions: 1304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1286
Number of HSP's successfully gapped: 222
Length of query: 437
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 340
Effective length of database: 4,167,664
Effective search space: 1417005760
Effective search space used: 1417005760
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: 59 (26.5 bits)