RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6208
(197 letters)
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 194 bits (494), Expect = 3e-58
Identities = 98/185 (52%), Positives = 131/185 (70%), Gaps = 3/185 (1%)
Query: 13 FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIK 72
F Y+K + L +P+ K + IV A+ F +V T PA + V T + P+
Sbjct: 108 FVDYVKEFLLG--KPISKGETVIVPVLEGALPFVVVSTQPAGFVYVTEATEVEIREKPV- 164
Query: 73 REEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTG 132
REE E V Y+DIGG ++ +I+EMVELP++HP LF+ +G++PP+G+LLYGPPGTG
Sbjct: 165 REEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTG 224
Query: 133 KTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 192
KTL+A+AVANE GA+F INGPEIMSK GESE LR+ F+EA++N+PSIIFIDE+DAIA
Sbjct: 225 KTLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIA 284
Query: 193 PKREK 197
PKRE+
Sbjct: 285 PKREE 289
Score = 144 bits (365), Expect = 3e-40
Identities = 61/113 (53%), Positives = 87/113 (76%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V + DIGG + +++E VE PL+HP +F+ +G++PP+G+LL+GPPGTGKTL+A+AVA
Sbjct: 450 VRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVAT 509
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E+GA F + GPEI+SK GESE +R+ F +A + +P+IIF DE+DAIAP R
Sbjct: 510 ESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPAR 562
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 169 bits (430), Expect = 3e-51
Identities = 68/129 (52%), Positives = 92/129 (71%)
Query: 67 EGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLY 126
E DP E E V Y+DIGG +Q+ +I+E+VELPL++P LF+ +G+ PP+G+LLY
Sbjct: 132 EVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLY 191
Query: 127 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID 186
GPPGTGKTL+A+AVAN+T A F + G E++ K GE +R+ FE A + +PSIIFID
Sbjct: 192 GPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFID 251
Query: 187 ELDAIAPKR 195
E+DAI KR
Sbjct: 252 EIDAIGAKR 260
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 159 bits (404), Expect = 2e-47
Identities = 68/129 (52%), Positives = 93/129 (72%)
Query: 67 EGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLY 126
E DP + E S V Y+DIGG +Q+ +++E VELPL+ P LF+ +G++PP+G+LLY
Sbjct: 112 EKDPRVQAMEVIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLY 171
Query: 127 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID 186
GPPGTGKTL+A+AVA+ET A F + G E++ K GE +R+ FE A + +PSIIFID
Sbjct: 172 GPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFID 231
Query: 187 ELDAIAPKR 195
E+DAIA KR
Sbjct: 232 EIDAIAAKR 240
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 148 bits (375), Expect = 2e-43
Identities = 70/133 (52%), Positives = 96/133 (72%)
Query: 63 VIHCEGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRG 122
V+ DP+ + E E V Y+DIGG +Q+ +I+E VELPL+HP LF+ +G++PP+G
Sbjct: 99 VLPTSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKG 158
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSI 182
+LLYGPPGTGKTL+A+AVA+ET A F + G E++ K GE +R+ FE A + +PSI
Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSI 218
Query: 183 IFIDELDAIAPKR 195
IFIDE+DAIA KR
Sbjct: 219 IFIDEIDAIAAKR 231
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 148 bits (376), Expect = 3e-43
Identities = 62/113 (54%), Positives = 79/113 (69%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V Y DIGG Q +I+E VELPL P L++ IG+ PPRG+LLYGPPGTGKT++A+AVA+
Sbjct: 142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAH 201
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
T A F + G E + K GE +R F A +N+PSIIFIDE+D+IA KR
Sbjct: 202 HTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKR 254
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 149 bits (377), Expect = 3e-43
Identities = 63/111 (56%), Positives = 84/111 (75%)
Query: 85 YDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANET 144
Y DIGG +Q+ +IKE VELPL HP L+ IG+KPP+G++LYGPPGTGKTL+A+AVANET
Sbjct: 182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET 241
Query: 145 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
A F + G E++ K G+ +R+ F A++N+PSI+FIDE+DAI KR
Sbjct: 242 SATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKR 292
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 143 bits (363), Expect = 8e-41
Identities = 61/114 (53%), Positives = 86/114 (75%)
Query: 82 AVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVA 141
V DDIGG + ++KE +E PL+ P LF+ +G++PP+G+LLYGPPGTGKTL+A+AVA
Sbjct: 238 DVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVA 297
Query: 142 NETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E+ + F + G E++SK GESE N+R+ FE+A K +PSIIFIDE+D++A R
Sbjct: 298 LESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGR 351
Score = 110 bits (277), Expect = 1e-28
Identities = 65/95 (68%), Positives = 80/95 (84%), Gaps = 1/95 (1%)
Query: 103 ELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG 162
ELPL+ P LFK +G++PP+G+LL+GPPGTGKTL+ARA+ANE GA F INGPEI+SK G
Sbjct: 1 ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVG 59
Query: 163 ESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 197
ESE LR+ FEEA+K +PSIIFIDE+DA+APKR
Sbjct: 60 ESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSS 94
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 132 bits (333), Expect = 2e-36
Identities = 61/140 (43%), Positives = 83/140 (59%), Gaps = 18/140 (12%)
Query: 70 PIKREEEE----EASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILL 125
I R E E E V Y DIGG Q+ QI++ VELP HP L++ G+KPP+G+LL
Sbjct: 162 AIPRTEVEDLVLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLL 221
Query: 126 YGPPGTGKTLIARAVANETG----------AFFFLINGPEIMSKLAGESESNLRKAFEEA 175
YGPPG GKTLIA+AVAN ++F I GPE+++K GE+E +R F+ A
Sbjct: 222 YGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRA 281
Query: 176 DK----NSPSIIFIDELDAI 191
+ P I+F DE+D++
Sbjct: 282 REKASEGRPVIVFFDEMDSL 301
>gnl|CDD|215649 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 = 120 bits (304), Expect = 2e-35
Identities = 44/74 (59%), Positives = 55/74 (74%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSI 182
+LLYGPPGTGKT +A+AVA E GA F I+G E++SK GESE LR+ FE A K +P +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 183 IFIDELDAIAPKRE 196
IFIDE+DA+A R
Sbjct: 61 IFIDEIDALAGSRG 74
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 123 bits (311), Expect = 3e-33
Identities = 53/119 (44%), Positives = 76/119 (63%), Gaps = 1/119 (0%)
Query: 77 EEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLI 136
E V + D+ G + ++ E+V+ L++PS F +G K P+G+LL GPPGTGKTL+
Sbjct: 46 NEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLL 104
Query: 137 ARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
A+AVA E G FF I+G + + G S +R FE+A KN+P IIFIDE+DA+ +R
Sbjct: 105 AKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQR 163
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 110 bits (277), Expect = 3e-29
Identities = 58/186 (31%), Positives = 95/186 (51%), Gaps = 11/186 (5%)
Query: 12 LFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPI 71
+F +Y + +L V + D FK++ P+ I+ + T+ E
Sbjct: 52 VFNIYARDQWLGEV--VREGDYLFDTRMFPDYAFKVIRVVPSGGGIITSTTIFVLETP-- 107
Query: 72 KREEEEEASNAVGYDDIGGCRKQLAQIK-EMVELPLRHPSLFKAIGVKPPRGILLYGPPG 130
REE+ E + + DD+ G ++ A+ K ++ L +P F G P+ +L YGPPG
Sbjct: 108 -REEDREIISDITLDDVIG--QEEAKRKCRLIMEYLENPERF---GDWAPKNVLFYGPPG 161
Query: 131 TGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 190
TGKT++A+A+ANE L+ E++ + G+ + + +E A K +P I+FIDELDA
Sbjct: 162 TGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDA 221
Query: 191 IAPKRE 196
IA R
Sbjct: 222 IALDRR 227
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 112 bits (281), Expect = 7e-29
Identities = 51/125 (40%), Positives = 76/125 (60%), Gaps = 1/125 (0%)
Query: 71 IKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPG 130
K + EA + + DI G + + +E+V L+ P F A+G K P+G+LL GPPG
Sbjct: 168 SKARFQMEADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPG 226
Query: 131 TGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 190
TGKTL+A+A+A E FF I+G E + G + +R F++A +NSP I+FIDE+DA
Sbjct: 227 TGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDA 286
Query: 191 IAPKR 195
+ +R
Sbjct: 287 VGRQR 291
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 109 bits (274), Expect = 5e-28
Identities = 53/127 (41%), Positives = 79/127 (62%), Gaps = 1/127 (0%)
Query: 69 DPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGP 128
K + E V + D+ G + ++ E+V+ L++P ++A+G K P+G+LL GP
Sbjct: 133 GKSKAKLYLEDQVKVTFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGP 191
Query: 129 PGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
PGTGKTL+A+AVA E G FF I+G + + G S +R FE+A KN+P IIFIDE+
Sbjct: 192 PGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEI 251
Query: 189 DAIAPKR 195
DA+ +R
Sbjct: 252 DAVGRQR 258
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 105 bits (262), Expect = 2e-26
Identities = 50/111 (45%), Positives = 73/111 (65%), Gaps = 1/111 (0%)
Query: 85 YDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANET 144
+ D+ GC + ++ E+VE LR PS F+ +G K P+G+L+ GPPGTGKTL+A+A+A E
Sbjct: 151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA 209
Query: 145 GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
FF I+G + + G S +R FE+A K +P IIFIDE+DA+ +R
Sbjct: 210 KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQR 260
>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 = 81.4 bits (201), Expect = 6e-20
Identities = 37/89 (41%), Positives = 56/89 (62%), Gaps = 6/89 (6%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTLIARAVANET---GAFFFLINGPEIMSKLAGESE-- 165
L +A+ + PP+ +LLYGPPGTGKT +ARA+ANE GA F +N +++ L
Sbjct: 10 LREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFG 69
Query: 166 -SNLRKAFEEADKNSPSIIFIDELDAIAP 193
+R FE A+K P ++FIDE+D+++
Sbjct: 70 HFLVRLLFELAEKAKPGVLFIDEIDSLSR 98
>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 = 66.6 bits (162), Expect = 3e-14
Identities = 30/94 (31%), Positives = 44/94 (46%), Gaps = 17/94 (18%)
Query: 119 PPRGILLYGPPGTGKTLIARAVANE---TGAFFFLINGPEIMS--------------KLA 161
P IL+ GPPG+GKT +ARA+A E G I+G +I+ K +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 162 GESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
G E LR A A K P ++ +DE+ ++
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAE 94
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 65.9 bits (162), Expect = 7e-13
Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRK 170
L + I ++L+GPPGTGKT +AR +A T A F ++ +G + LR+
Sbjct: 27 LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAV-----TSGVKD--LRE 79
Query: 171 AFEEADKNSPS----IIFIDE 187
EEA + + I+FIDE
Sbjct: 80 VIEEARQRRSAGRRTILFIDE 100
>gnl|CDD|215011 smart01072, CDC48_2, Cell division protein 48 (CDC48) domain 2.
This domain has a double psi-beta barrel fold and
includes VCP-like ATPase and N-ethylmaleimide sensitive
fusion protein N-terminal domains. Both the VAT and NSF
N-terminal functional domains consist of two structural
domains of which this is at the C-terminus. The VAT-N
domain found in AAA ATPases is a substrate 185-residue
recognition domain.
Length = 64
Score = 57.6 bits (140), Expect = 9e-12
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 13 FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIK 72
F Y+K L RPV K D +V +A+ F +V T+P+ IV DT I P++
Sbjct: 6 FAEYVKRKLLG--RPVTKGDTIVVPFLGKALPFVVVSTEPSGPVIVTDDTEIEILEKPVE 63
Query: 73 R 73
Sbjct: 64 E 64
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 61.2 bits (149), Expect = 2e-11
Identities = 40/107 (37%), Positives = 59/107 (55%), Gaps = 9/107 (8%)
Query: 86 DDIGGCRKQLAQIKEMVELPLRHPSLFKA---IGVKPPRGILLYGPPGTGKTLIARAVAN 142
DIGG L +K+ L R S K G+ PRG+LL G GTGK+L A+A+AN
Sbjct: 228 SDIGG----LDNLKDW--LKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAN 281
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELD 189
+ ++ ++ + GESES +R+ A+ SP I++IDE+D
Sbjct: 282 DWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEID 328
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 59.6 bits (145), Expect = 1e-10
Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 11/81 (13%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRK 170
L +A+ ++L+GPPGTGKT +AR +A T A F ++ + S + +LR+
Sbjct: 39 LRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSA--VTSGVK-----DLRE 91
Query: 171 AFEEADKNSPS----IIFIDE 187
EEA KN I+F+DE
Sbjct: 92 IIEEARKNRLLGRRTILFLDE 112
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 53.9 bits (130), Expect = 9e-09
Identities = 28/69 (40%), Positives = 38/69 (55%), Gaps = 12/69 (17%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-----N 178
+LYGPPG GKT +AR +AN T A F +N + LAG + LR + A +
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLN-----AVLAGVKD--LRAEVDRAKERLERHG 108
Query: 179 SPSIIFIDE 187
+I+FIDE
Sbjct: 109 KRTILFIDE 117
>gnl|CDD|202475 pfam02933, CDC48_2, Cell division protein 48 (CDC48), domain 2.
This domain has a double psi-beta barrel fold and
includes VCP-like ATPase and N-ethylmaleimide sensitive
fusion protein N-terminal domains. Both the VAT and NSF
N-terminal functional domains consist of two structural
domains of which this is at the C-terminus. The VAT-N
domain found in AAA ATPases pfam00004 is a substrate
185-residue recognition domain.
Length = 61
Score = 47.2 bits (113), Expect = 7e-08
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 13 FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDP 70
Y K F +PV K + + + +V T+P+ IV DT I P
Sbjct: 6 ELAYFKRQFEG--QPVSKGQTIVFDFLGKLLPLVVVSTEPSGPVIVTEDTEIEIGEKP 61
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 50.6 bits (122), Expect = 1e-07
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 12/73 (16%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSP 180
+LL+GPPG GKT +A +ANE G + +GP + LA + EE D
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPGDLA-----AILTNLEEGD---- 105
Query: 181 SIIFIDELDAIAP 193
++FIDE+ ++P
Sbjct: 106 -VLFIDEIHRLSP 117
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. All
proteins in this family for which functions are known
are 5'-3' DNA helicases that, as part of a complex with
RuvA homologs serve as a 5'-3' Holliday junction
helicase. RuvA specifically binds Holliday junctions as
a sandwich of two tetramers and maintains the
configuration of the junction. It forms a complex with
two hexameric rings of RuvB, the subunit that contains
helicase activity. The complex drives ATP-dependent
branch migration of the Holliday junction recombination
intermediate. The endonuclease RuvC resolves junctions
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 305
Score = 49.2 bits (118), Expect = 2e-07
Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 12/76 (15%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSP 180
+LLYGPPG GKT +A +ANE G + +GP + LA + EE D
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAA-----ILTNLEEGD---- 83
Query: 181 SIIFIDELDAIAPKRE 196
++FIDE+ ++P E
Sbjct: 84 -VLFIDEIHRLSPAVE 98
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 47.8 bits (115), Expect = 9e-07
Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 12/73 (16%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNSP 180
+LLYGPPG GKT +A +ANE G + +GP + LA +NL EE D
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLAA-ILTNL----EEGD---- 104
Query: 181 SIIFIDELDAIAP 193
++FIDE+ ++P
Sbjct: 105 -VLFIDEIHRLSP 116
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 47.3 bits (113), Expect = 1e-06
Identities = 27/59 (45%), Positives = 35/59 (59%), Gaps = 5/59 (8%)
Query: 98 IKEMVELPLRHPSLFKAIGVKPPR--GILLYGP-PGTGKTLIARAVANETGAFFFLING 153
I E + LP FK+I VK R +LL+ P PGTGKT +A+A+ NE GA +NG
Sbjct: 20 IDECI-LPAADKETFKSI-VKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNG 76
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 45.9 bits (109), Expect = 3e-06
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 13/77 (16%)
Query: 120 PRGILLYGPPGTGKTLIARAVANE---TGAFFFLINGPEIMSKLA-----GESESNLRKA 171
++L GPPG GKT +A A+ NE G I P+++SKL G E L +
Sbjct: 105 GENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLRE 164
Query: 172 FEEADKNSPSIIFIDEL 188
++ D ++ ID++
Sbjct: 165 LKKVD-----LLIIDDI 176
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 46.1 bits (110), Expect = 3e-06
Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 14/84 (16%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFFLI--NGP-----EIMSKLAGESESNLRK 170
KP + +LLYGPPG GKT +A A+AN+ G + +I N +++ ++AGE+ +
Sbjct: 37 KPKKALLLYGPPGVGKTSLAHALANDYG--WEVIELNASDQRTADVIERVAGEA-ATSGS 93
Query: 171 AFEEADKNSPSIIFIDELDAIAPK 194
F K +I +DE+D I
Sbjct: 94 LFGARRK----LILLDEVDGIHGN 113
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 46.2 bits (110), Expect = 4e-06
Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 5/56 (8%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGA--FFFLINGPEIMSKLAGESES---NLRKA 171
RGIL+ GPPGTGKT +A +A E G F I+G EI S ++E+ LR+A
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQALRRA 121
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 45.6 bits (108), Expect = 6e-06
Identities = 35/155 (22%), Positives = 56/155 (36%), Gaps = 16/155 (10%)
Query: 49 DTDPAPYCIVAADTVIHCEGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRH 108
D AP D + E E E + +G + + ++Q+A +K + L
Sbjct: 245 DPSSAPSRAEFVDPAAAERKAKLLAEAEAELAEQIGLERV---KRQVAALKSSTAMALAR 301
Query: 109 PSLFKAIGVKPP---RGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM----SKLA 161
G+ +L GPPGTGKT IAR VA ++ P + + L
Sbjct: 302 ----AERGLPVAQTSNHMLFAGPPGTGKTTIARVVAKIY-CGLGVLRKPLVREVSRADLI 356
Query: 162 GESESNLRKAFEEA-DKNSPSIIFIDELDAIAPKR 195
G+ E D ++F+DE +
Sbjct: 357 GQYIGESEAKTNEIIDSALGGVLFLDEAYTLVETG 391
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 45.4 bits (108), Expect = 7e-06
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAF--FFLINGPEIMSKLAGESES---NLRKA 171
R +L+ GPPGTGKT +A A++ E G F I+G E+ S ++E+ RKA
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTEALTQAFRKA 106
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 44.3 bits (105), Expect = 1e-05
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFFLING-PEIM-SKLAGESESNLRKAFEEADK- 177
+LL GPPG GKTL+ARA+A G F I P+++ S L G +
Sbjct: 44 GHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRF 103
Query: 178 -------NSPSIIFIDELDAIAPK 194
I+ +DE++ P+
Sbjct: 104 VPGPLFAAVRVILLLDEINRAPPE 127
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 42.2 bits (100), Expect = 3e-05
Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 13/84 (15%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAF---FFLINGPEIM-----SKLAGESESNLRKA--- 171
L GP G GKT +A+A+A I+ E M S+L G +
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 172 --FEEADKNSPSIIFIDELDAIAP 193
E + SI+ IDE++ P
Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKAHP 89
>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 = 42.4 bits (101), Expect = 5e-05
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 12/67 (17%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNSP 180
+LLYGPPG GKT +A +ANE G + +GP + LA + E D
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLAA-----ILTNLEPGD---- 103
Query: 181 SIIFIDE 187
++FIDE
Sbjct: 104 -VLFIDE 109
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 42.2 bits (100), Expect = 7e-05
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 97 QIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
QI+E+ + +L + P + +YG GTGKT + + V E
Sbjct: 23 QIEELAK------ALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKE 63
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 41.7 bits (98), Expect = 1e-04
Identities = 30/80 (37%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM-SKLAGESESN-LRKAFEEAD---- 176
ILL GP G+GKTL+A+ +A F + + + + GE N L K + AD
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 177 KNSPSIIFIDELDAIAPKRE 196
K II+IDE+D I+ K E
Sbjct: 179 KAQKGIIYIDEIDKISRKSE 198
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 40.8 bits (96), Expect = 2e-04
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 121 RGILLYGPPGTGKTLIARAVANE 143
G+LL+G GTGKT +A +ANE
Sbjct: 115 VGLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 40.7 bits (96), Expect = 2e-04
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 24/86 (27%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLING--PEIMS----------------KLAGESE 165
+L G PG GKT I +A ++NG PE + K GE E
Sbjct: 195 VLVGEPGVGKTAIVEGLAQR------IVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFE 248
Query: 166 SNLRKAFEEADKNSPSIIFIDELDAI 191
L+ +E +K+ I+FIDE+ I
Sbjct: 249 ERLKAVLKEVEKSKNVILFIDEIHTI 274
Score = 30.7 bits (70), Expect = 0.50
Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 17/87 (19%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVA---NETGAFFFLINGPEIM-----SKLAGESESNLR 169
+P L GP G GKT +A+A+A I+ E M S+L G +
Sbjct: 519 RPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYV- 577
Query: 170 KAFEEA-------DKNSPSIIFIDELD 189
+EE + S+I +DE++
Sbjct: 578 -GYEEGGQLTEAVRRKPYSVILLDEIE 603
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 38.4 bits (90), Expect = 4e-04
Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 16/94 (17%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANET-GAFFFLINGP------EIMSKLAGE------ 163
+ +L G G+GKT + R +A + + P +++ K+
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLS 60
Query: 164 --SESNLRKAFEEADKNSPS-IIFIDELDAIAPK 194
+ + L +A +A K ++ IDE ++ +
Sbjct: 61 GGTTAELLEAILDALKRRGRPLLIIDEAQHLSLE 94
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 38.4 bits (90), Expect = 5e-04
Identities = 22/85 (25%), Positives = 33/85 (38%), Gaps = 18/85 (21%)
Query: 122 GILLYGPPGTGKTLIARAVANET-GAFFFLINGP------------EIMSKLAGESESNL 168
G+LL GPPGTGK+ +A +A F + I A + L
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60
Query: 169 RKAFEEADKNSPSIIFIDELDAIAP 193
+A E + I +DE++ P
Sbjct: 61 VRAAREGE-----IAVLDEINRANP 80
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 38.7 bits (90), Expect = 5e-04
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 91 CR-KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
R ++L ++ + + P +LL GP GTGKT + R +
Sbjct: 4 GREEELERLLD----------ALRRARSGGPPSVLLTGPSGTGKTSLLRELLEG 47
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 38.9 bits (91), Expect = 8e-04
Identities = 24/100 (24%), Positives = 38/100 (38%), Gaps = 22/100 (22%)
Query: 120 PRGILLYGPPGTGKTLIARAVANE-----TGAFFFLING----------PEIMSKLAGES 164
P I++YGP GTGKT + V E IN +I++KL
Sbjct: 42 PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVP 101
Query: 165 ESNLR--KAFEEADKN-----SPSIIFIDELDAIAPKREK 197
+ + + N I+ +DE+DA+ K +
Sbjct: 102 LTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGE 141
>gnl|CDD|216186 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 = 36.4 bits (85), Expect = 0.001
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK 159
I LYGPPG GK+ +A+ +A L + S+
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSR 37
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 38.1 bits (89), Expect = 0.002
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 117 VKPPRG-ILLYGPPGTGKTLIARAVAN 142
R + YGP TGKT +A+A+A+
Sbjct: 109 QGGKRNTVWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 36.5 bits (84), Expect = 0.002
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
IL+ GPPG+GK+ +A+ +A + G
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVI 28
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 37.4 bits (88), Expect = 0.003
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 20/87 (22%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM--------SKLAGES-ESNLRKAFE 173
ILL GP G+GKTL+A+ +A +++ P + + GE E+ L K +
Sbjct: 111 ILLIGPTGSGKTLLAQTLAR-------ILDVPFAIADATTLTEAGYVGEDVENILLKLLQ 163
Query: 174 EAD----KNSPSIIFIDELDAIAPKRE 196
AD K I++IDE+D IA K E
Sbjct: 164 AADYDVEKAQRGIVYIDEIDKIARKSE 190
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 37.2 bits (87), Expect = 0.003
Identities = 31/87 (35%), Positives = 43/87 (49%), Gaps = 20/87 (22%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK--------LAGESESN-LRKAFE 173
ILL GP G+GKTL+A+ +A ++N P ++ GE N L K +
Sbjct: 100 ILLIGPTGSGKTLLAQTLAK-------ILNVPFAIADATTLTEAGYVGEDVENILLKLLQ 152
Query: 174 EADKNSP----SIIFIDELDAIAPKRE 196
AD + II+IDE+D IA K E
Sbjct: 153 AADYDVERAERGIIYIDEIDKIARKSE 179
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 36.4 bits (85), Expect = 0.005
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 19/84 (22%)
Query: 123 ILLYGPPGTGKTLIARAVANE-------TGAFFFLINGPEIM---SKLAGESESNLRKAF 172
L+ G PGTGKT++A + E A F N P ++ LAG+ + +K F
Sbjct: 4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKKLF 63
Query: 173 EEA-------DKNSPS--IIFIDE 187
+ K P ++ +DE
Sbjct: 64 RKPTSFINNLHKAPPHEDVVIVDE 87
>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 = 36.0 bits (84), Expect = 0.006
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 123 ILLYGPPGTGKTLIARA 139
+L+ GPPG+GKT++A+
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 36.4 bits (85), Expect = 0.006
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
+ L GPPG GKT + +++A G F
Sbjct: 353 LCLVGPPGVGKTSLGKSIAKALGRKFV 379
>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 = 34.8 bits (81), Expect = 0.007
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFF 148
+LL G PG KTL+AR +A G F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 35.9 bits (82), Expect = 0.010
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLR---KAFEEADKNS 179
+ L G G+GK IA +A F+ +N +L G ++N + F EA K
Sbjct: 122 VFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKG 181
Query: 180 PSIIFIDELDAIAPK 194
+ FIDE+DA P+
Sbjct: 182 -GLFFIDEIDASIPE 195
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 34.3 bits (79), Expect = 0.010
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
IL+ G PG+GKT +A+ +A G
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLR 27
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 36.1 bits (83), Expect = 0.010
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLIN 152
+ +A+ V + ILL G PG GKT + A+A +TG IN
Sbjct: 1536 VLRAMQVG--KPILLEGSPGVGKTSLITALARKTGKKLIRIN 1575
Score = 29.6 bits (66), Expect = 1.5
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPE 155
+L+ GP +GKT + +A ETG F IN E
Sbjct: 891 LLIQGPTSSGKTSMILYLARETGHKFVRINNHE 923
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 35.7 bits (83), Expect = 0.010
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLI 151
+ L GPPG GKT + +++A F
Sbjct: 350 LCLVGPPGVGKTSLGKSIAKALNRKFVRF 378
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 35.5 bits (82), Expect = 0.014
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 4/97 (4%)
Query: 92 RKQLAQIKEMVELPLRH-PSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFL 150
++ + IK+ + P L K + ++P IL+ GP GKT + + +
Sbjct: 9 IEEDSDIKKWEIERRKLLPRLIKKLDLRPFI-ILILGPRQVGKTTLLKLLIKGLLEEIIY 67
Query: 151 INGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDE 187
IN ++ +L +A+ E + S IF+DE
Sbjct: 68 INFDDLRLD--RIELLDLLRAYIELKEREKSYIFLDE 102
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 35.2 bits (81), Expect = 0.016
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 120 PRGILLYGPPGTGKTLIARAVANE 143
P+ I+LYGPPG GKT AR E
Sbjct: 175 PQHIILYGPPGVGKTTAARLALEE 198
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 35.2 bits (82), Expect = 0.017
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 97 QIKEMVELPLRHPSLFKAI-GVKPPRGILLYGPPGTGKTLIARAVANE 143
QI+E+ LR A+ G +P +L+YGPPGTGKT + V E
Sbjct: 38 QIEELAFA-LRP-----ALRGSRPLN-VLIYGPPGTGKTTTVKKVFEE 78
>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 = 35.2 bits (81), Expect = 0.017
Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 14/83 (16%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----------LINGPEIMSKLAGE--- 163
K R +LL G PG GK+++A+A+A N P I+ AGE
Sbjct: 34 AKQKRNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPEDPNMPRIVEVPAGEGRE 93
Query: 164 -SESNLRKAFEEADKNSPSIIFI 185
E +KAF++ + + I
Sbjct: 94 IVEDYKKKAFKQPSSRNLLLFMI 116
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 34.9 bits (81), Expect = 0.018
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANE 143
K +L YG GTGKT ++ +A E
Sbjct: 181 KNNENLLFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 34.2 bits (79), Expect = 0.019
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 123 ILLYGPPGTGKTLIAR------AVANETGAFFFLINGPEIMSKLAGESESNLRKAFEE 174
LL G PGTGKT A E G + L PE + + A +L + E+
Sbjct: 2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWDLER-LED 58
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 35.0 bits (81), Expect = 0.019
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 9/51 (17%)
Query: 93 KQLAQIKEMVEL-------PLRHPSLFKAIG--VKPPRGILLYGPPGTGKT 134
Q A + L +L G P RG+ L+G G GKT
Sbjct: 29 AQPAAAAALDRLYDELVAPRSARKALGWLFGRDHGPVRGLYLWGGVGRGKT 79
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins.
Length = 162
Score = 34.3 bits (79), Expect = 0.020
Identities = 25/106 (23%), Positives = 33/106 (31%), Gaps = 21/106 (19%)
Query: 106 LRHPSLFKAIGVKPPRGIL--LYGPPGTGKTLIARAVA-NETGAFFFLINGPE------- 155
R PS F V G L + GP G+GK+ I A+ GA
Sbjct: 5 GRFPSYFVPNDVTFGEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIV 64
Query: 156 ----------IMSKLAGESE-SNLRKAFEEADKNSPSIIFIDELDA 190
+ GE E S L A + +DE+D
Sbjct: 65 AAVSAELIFTRLQLSGGEKELSALALILALASLKPRPLYILDEIDR 110
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 34.3 bits (79), Expect = 0.025
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 116 GVKPPRGILLYGPPGTGKTLIARAVANETG 145
+K P IL+ G G GK+ IA +A G
Sbjct: 85 KMKRPLIILIGGASGVGKSTIAGELARRLG 114
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 34.5 bits (80), Expect = 0.028
Identities = 16/29 (55%), Positives = 19/29 (65%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFF 148
P+ IL+ GP G GKT IAR +A GA F
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLAGAPF 78
Score = 26.8 bits (60), Expect = 7.3
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 154 PEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 194
E KL + E ++A + A++N I+FIDE+D IA +
Sbjct: 228 EEEADKLI-DQEEIKQEAIDAAEQNG--IVFIDEIDKIAKR 265
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 33.5 bits (78), Expect = 0.034
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 18/80 (22%)
Query: 123 ILLYGPPGTGKTLIARAVANET---GAFFFLING---PE--IMSKLAGESE------SNL 168
+L+ G GTGK L ARA+ + F +N PE + S+L G + +
Sbjct: 25 VLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVSD 84
Query: 169 RK-AFEEADKNSPSIIFIDE 187
RK FE AD +F+DE
Sbjct: 85 RKGLFELADG---GTLFLDE 101
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 34.2 bits (79), Expect = 0.037
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAF-----FFLINGPEIMSKLAGESESNLRKAFEEADK 177
+ +YG G GKT + +A+ NE A + + + N + F+E K
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKE--K 173
Query: 178 NSPSIIFIDELDAIAPKREK 197
S ++ ID++ +A K
Sbjct: 174 YSLDLLLIDDIQFLAGKERT 193
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 32.5 bits (75), Expect = 0.042
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAF-FFLINGPEIMSKLAGESESNLRKAFEEADKNSPS 181
I++ GP GKT + E + IN + + + +L + F +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDP--RFLRLALLDLLEEFLKLLLPGKK 62
Query: 182 IIFIDE 187
+F+DE
Sbjct: 63 YLFLDE 68
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 33.6 bits (77), Expect = 0.042
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFFLING 153
+ L GP GTGKT +A VA + LING
Sbjct: 22 YPVHLRGPAGTGKTTLAMHVARKRDRPVMLING 54
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 33.2 bits (76), Expect = 0.043
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESE 165
R +L+ G PG+GK+ +AR +A GA + I +L G E
Sbjct: 1 GRLVLVGGLPGSGKSTLARGLAELLGA--IRLRSDVIRKRLFGVPE 44
>gnl|CDD|238260 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 = 32.9 bits (76), Expect = 0.043
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I+L G G GKT + R +A G F
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 34.0 bits (78), Expect = 0.046
Identities = 34/119 (28%), Positives = 54/119 (45%), Gaps = 27/119 (22%)
Query: 94 QLAQIKEMVELPLRHPSLFKAIGVKPPR---GILLYGPPGTGKTLIARAVANETGAFFFL 150
QLA++ + L R L +AI V R LL G G GKT IA +A + +
Sbjct: 178 QLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLA------WRI 231
Query: 151 ING--PEIM----------------SKLAGESESNLRKAFEEADKNSPSIIFIDELDAI 191
+ G PE+M +K G+ E + ++ ++++ SI+FIDE+ I
Sbjct: 232 VQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTI 290
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 33.8 bits (78), Expect = 0.048
Identities = 33/151 (21%), Positives = 55/151 (36%), Gaps = 30/151 (19%)
Query: 1 MKLVPEGEMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAA 60
+ +V GE S L EV L +P+ +D + G V V D ++
Sbjct: 163 LDVVSAGEDSTLLEV------LRTGKPI-RDVVQTYNGNKIIVNVAPVYADGQ---LIGV 212
Query: 61 DTVIHCEGDPIKREEEE--------EASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLF 112
+ + ++R E +DDI G + ++ E+ + + S
Sbjct: 213 VGISK-DVSELERLTRELEESEGLLRLKAKYTFDDIIGESPAMLRVLELAKRIAKTDS-- 269
Query: 113 KAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
+L+ G GTGK L ARA+ N
Sbjct: 270 ---------TVLILGESGTGKELFARAIHNL 291
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 32.6 bits (75), Expect = 0.055
Identities = 30/88 (34%), Positives = 39/88 (44%), Gaps = 16/88 (18%)
Query: 120 PRG--ILLYGPPGTGKTL----IARAVANETGAFFFLINGPEIMSKL--AGE-SESNLRK 170
PRG LL G PGTGK+ +A AVA TG F E L GE SE+ LR+
Sbjct: 31 PRGGLTLLAGAPGTGKSTLALDLAAAVA--TGRPFLGPFPVEPGRVLYLDGEDSEAGLRR 88
Query: 171 AFEEADK-----NSPSIIFIDELDAIAP 193
+ P ++ ID L ++
Sbjct: 89 RLRALGEALEEIEGPDLVVIDPLASLLG 116
>gnl|CDD|238978 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 = 32.5 bits (75), Expect = 0.059
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 127 GPPGTGKTLIARAVANETGAFFF---LINGPEIMSKLA 161
GP G+GK+ +A+ +A + G + I E+ KLA
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLDTGGIRTEEV-GKLA 42
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 33.7 bits (77), Expect = 0.060
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 115 IGVKPPRGILLYGPPGTGKTLIARAVA 141
+ + P RGIL+ G GTG++ + + +A
Sbjct: 1625 LALSPSRGILVIGSIGTGRSYLVKYLA 1651
>gnl|CDD|237965 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator
FhlA; Provisional.
Length = 686
Score = 33.3 bits (76), Expect = 0.070
Identities = 32/87 (36%), Positives = 42/87 (48%), Gaps = 30/87 (34%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL------AGESESNL----RKA- 171
+L+ G GTGK LIARA+ N +G N M K+ AG ES+L R A
Sbjct: 402 VLILGETGTGKELIARAIHNLSGR-----NNRR-MVKMNCAAMPAGLLESDLFGHERGAF 455
Query: 172 ----------FEEADKNSPSIIFIDEL 188
FE ADK+S +F+DE+
Sbjct: 456 TGASAQRIGRFELADKSS---LFLDEV 479
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 32.8 bits (75), Expect = 0.076
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 121 RGIL--LYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEE-ADK 177
RG + +YGPPGTGKT IA +A ET + G S R+ + ++
Sbjct: 18 RGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKV----AYIDTEGLSSERFRQIAGDRPER 73
Query: 178 NSPSIIFIDELD 189
+ SII + +D
Sbjct: 74 AASSIIVFEPMD 85
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 32.5 bits (75), Expect = 0.077
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 20/75 (26%)
Query: 127 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE-----------SESNL------- 168
GPPG+GKT +AR +A + G ++ EI +LA E +E +
Sbjct: 7 GPPGSGKTTVARLLAEKLG--LKHVSAGEIFRELAKERGMSLEEFNKYAEEDPEIDKEID 64
Query: 169 RKAFEEADKNSPSII 183
R+ E A+K ++
Sbjct: 65 RRQLEIAEKEDNVVL 79
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 32.7 bits (75), Expect = 0.085
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 124 LLYGPPGTGKTLIARAVANET 144
L+ GPPG+GKT RA+A E
Sbjct: 40 LVQGPPGSGKTAAVRALAREL 60
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.9 bits (76), Expect = 0.090
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 121 RGILLYGPPGTGKTLIARAVAN 142
GIL+ G PG GK+ A+A+A
Sbjct: 258 EGILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 32.8 bits (75), Expect = 0.10
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 120 PRGILLYGPPGTGKTLIARAVANE 143
P+ +++YGPPG GKT AR V E
Sbjct: 86 PQHVIIYGPPGVGKTAAARLVLEE 109
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 32.3 bits (74), Expect = 0.11
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 93 KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGK-TLIARAVANETGAFFFLI 151
+Q + +++ E L P + + PP +++ GPPG GK TLI + T I
Sbjct: 12 RQFQRTQDLEEKKLHVPVVDRTPEEPPPLVVVVVGPPGVGKSTLIRSLIKRYTKQNLSDI 71
Query: 152 NGP 154
GP
Sbjct: 72 KGP 74
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 32.7 bits (75), Expect = 0.11
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 121 RGILLYGPPGTGKTLIARAVAN 142
GIL+ G PG GK+ A+A+A
Sbjct: 264 EGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 31.7 bits (73), Expect = 0.12
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFF 149
I+L G G GK+ I R +A G F
Sbjct: 2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 32.3 bits (74), Expect = 0.14
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 17/82 (20%)
Query: 69 DPIKREEEEEASNAVGYDDIGGCRKQLA-QIKEMVE---LPLRHPS---LFKAIGVKPPR 121
+ + + E+ A G R + L LR P L + +
Sbjct: 367 EAAQMDTEKPART--------GRRIDFDDNADHGITLENLSLRTPDGQTLLSELNFEVRP 418
Query: 122 G--ILLYGPPGTGKTLIARAVA 141
G +L+ G G GKT + RA+A
Sbjct: 419 GERLLITGESGAGKTSLLRALA 440
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 32.2 bits (74), Expect = 0.15
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+L GPPGTGKT A A+A E
Sbjct: 41 LLFAGPPGTGKTTAALALARE 61
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 32.1 bits (73), Expect = 0.15
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFF 148
P+ IL+ GP G GKT IAR +A A F
Sbjct: 47 PKNILMIGPTGVGKTEIARRLAKLANAPF 75
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 32.3 bits (74), Expect = 0.16
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 121 RGILLYGPPGTGKTLIARAVA-----------NETGAFFFLINGPEIM-SKLAGESESNL 168
+L G PG GKT IA +A E L G + +K GE E L
Sbjct: 201 NNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERL 260
Query: 169 RKAFEEADKNSPSIIFIDE 187
++ F+E +N+ I+ IDE
Sbjct: 261 KRIFDEIQENNNIILVIDE 279
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 32.2 bits (74), Expect = 0.16
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 9/33 (27%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFFLING 153
R L+ G GTGKTL A FL+NG
Sbjct: 32 RPTLVSGTAGTGKTLF---------ALQFLVNG 55
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 31.5 bits (72), Expect = 0.16
Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 11/83 (13%)
Query: 124 LLYGPPGTGKTLIA-----RAVANETGAFFFLINGPEI--MSKLAGESESNLRKAFEEAD 176
L+ G PG+GKTL A + I+G + K+ GE + D
Sbjct: 4 LITGKPGSGKTLEAVSYHILPALKKGRKVITNIDGLNLERFPKVFGEDVRERLEDIGYMD 63
Query: 177 K--NSP--SIIFIDELDAIAPKR 195
P +++ IDE P R
Sbjct: 64 PWRTYPKGALLVIDEAQTWFPSR 86
>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed.
Length = 790
Score = 32.4 bits (73), Expect = 0.17
Identities = 32/98 (32%), Positives = 46/98 (46%), Gaps = 21/98 (21%)
Query: 120 PRG--ILLYGPPGTGKTLIA-RAVAN--ETGAFFFLING-----PEIMSKLAGESESNL- 168
PRG I +YGP +GKT +A AVAN G I+ P+ KL +++S L
Sbjct: 58 PRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLV 117
Query: 169 ------RKAFEEAD----KNSPSIIFIDELDAIAPKRE 196
+A E AD + I+ ID + A+ P+ E
Sbjct: 118 SQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAE 155
>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 = 32.0 bits (73), Expect = 0.17
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 123 ILLYGPPGTGKTLIARAVA 141
+L+ G GTGK L AR +
Sbjct: 104 VLIIGETGTGKELFARLIH 122
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 31.8 bits (73), Expect = 0.19
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 121 RGILLYGPPGTGKTLIAR 138
+LL GPPGTGKT++A
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 31.6 bits (72), Expect = 0.21
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 124 LLYGPPGTGKTLIARAVANETGA 146
L++G TGKT A A+A ETG
Sbjct: 5 LIWGATCTGKTAEAIALAKETGW 27
>gnl|CDD|237963 PRK15424, PRK15424, propionate catabolism operon regulatory protein
PrpR; Provisional.
Length = 538
Score = 32.0 bits (73), Expect = 0.21
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 15/69 (21%)
Query: 86 DDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG 145
D+ G Q+ Q+++ + L R + +L+ G GTGK L A+A+ E
Sbjct: 219 GDLLGQSPQMEQVRQTILLYARSSA-----------AVLIQGETGTGKELAAQAIHRE-- 265
Query: 146 AFFFLINGP 154
+F +
Sbjct: 266 --YFARHDA 272
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 31.6 bits (71), Expect = 0.23
Identities = 14/32 (43%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 110 SLFKAIGVKPPRGILLYGPPGTGKTLIARAVA 141
++ K + +K + I+L GPPG GKT +AR +A
Sbjct: 186 TILKRLTIK--KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 31.1 bits (71), Expect = 0.23
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGA 146
P +LL G PG GKT +ARA+ E G
Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELGG 38
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 31.7 bits (72), Expect = 0.24
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVA 141
+KP R LL GPP +GKT + A+A
Sbjct: 188 IKPSRMTLLLGPPSSGKTTLLLALA 212
>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 = 31.7 bits (72), Expect = 0.24
Identities = 10/16 (62%), Positives = 15/16 (93%)
Query: 123 ILLYGPPGTGKTLIAR 138
+LL+GPPG+GKT++A
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC transporters
are a large family of proteins involved in the transport
of a wide variety of different compounds including
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 = 202
Score = 31.1 bits (71), Expect = 0.24
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 99 KEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF 147
K ++P+ VKP +L+ G PG+G + + +A+AN T
Sbjct: 15 KGRSKIPILKDFSGV---VKPGEMVLVLGRPGSGCSTLLKALANRTEGN 60
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 31.1 bits (71), Expect = 0.24
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVA 141
+ L GP G GK L+A A+A
Sbjct: 12 RLAHAYLFAGPEGVGKELLALALA 35
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 31.4 bits (72), Expect = 0.27
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 121 RGILLYGPPGTGKTLIARAVANE 143
+G+ LYG G GK+ + A+ANE
Sbjct: 157 KGLYLYGDFGVGKSYLLAAIANE 179
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 30.9 bits (70), Expect = 0.27
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE 163
I + GPPG+GKT +A+ +A + LI+ +I +LA +
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLS--LKLISAGDIFRELAAK 41
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.8 bits (70), Expect = 0.28
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE 163
I + G PG+GKT +AR +A G L++ I ++A E
Sbjct: 3 ITISGLPGSGKTTVARELAEHLG--LKLVSAGTIFREMARE 41
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 30.4 bits (69), Expect = 0.28
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE 163
IL+ G PG+GK+ AR + E GA +++ + +L G+
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGA--VVLSSDTLRKRLRGD 40
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 31.4 bits (71), Expect = 0.29
Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 30/99 (30%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFF---FLINGPEIMSKLAGESESN---------L 168
R + ++G G GKT IARA+ + F I+ I + S +N L
Sbjct: 208 RMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHL 267
Query: 169 RKAF------------------EEADKNSPSIIFIDELD 189
++AF EE K+ +IFID+LD
Sbjct: 268 QRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLD 306
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 31.5 bits (72), Expect = 0.30
Identities = 10/21 (47%), Positives = 18/21 (85%)
Query: 121 RGILLYGPPGTGKTLIARAVA 141
R +++ G PGTGK+++A+A+A
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|238540 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 = 30.5 bits (69), Expect = 0.36
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 123 ILLYGPPGTGKTLIARAVAN 142
IL++GP G+GKT +A +A
Sbjct: 2 ILVFGPTGSGKTTLALQLAL 21
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.9 bits (70), Expect = 0.37
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 101 MVELPLRHPSLFKAIGVKPPRG--ILLYGPPGTGKTLIARAVANE 143
M +P P L + +G PRG +L+ GPPGTGKT+ A E
Sbjct: 2 MERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYE 46
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.1 bits (71), Expect = 0.37
Identities = 25/80 (31%), Positives = 34/80 (42%), Gaps = 12/80 (15%)
Query: 124 LLYGPPGTGKTLIARAVAN--ETGAFFFLINGPEIMS----------KLAGESESNLRKA 171
LL G PG GKT I +A G + +I S K G+ E L+
Sbjct: 206 LLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAV 265
Query: 172 FEEADKNSPSIIFIDELDAI 191
E +K +I+FIDE+ I
Sbjct: 266 VSEIEKEPNAILFIDEIHTI 285
Score = 30.0 bits (68), Expect = 0.84
Identities = 16/42 (38%), Positives = 20/42 (47%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK 159
KP L GP G GKT +A+ +A E G + E M K
Sbjct: 481 KPVGSFLFVGPTGVGKTELAKQLAEELGVHLLRFDMSEYMEK 522
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 30.4 bits (69), Expect = 0.43
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 5/28 (17%)
Query: 124 LLYGPPGTGKT-----LIARAVANETGA 146
L+ GPPGTGKT +I + ++N G
Sbjct: 21 LIQGPPGTGKTTTIVEIIKQLLSNAPGK 48
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 30.3 bits (69), Expect = 0.43
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 123 ILLYGPPGTGKT 134
+L+YGPPG GKT
Sbjct: 6 VLIYGPPGIGKT 17
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 30.5 bits (69), Expect = 0.44
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 18/82 (21%)
Query: 127 GPPGTGKTLIARAVANETGAFFFLINGPEIMSK----------LAGESESNL-RKAFEEA 175
G PGTGKT +AR + G F +N ++SK L GE + +K E
Sbjct: 49 GNPGTGKTTVARIL----GKLFKEMN---VLSKGHLIEVERADLVGEYIGHTAQKTREVI 101
Query: 176 DKNSPSIIFIDELDAIAPKREK 197
K ++FIDE ++A EK
Sbjct: 102 KKALGGVLFIDEAYSLARGGEK 123
>gnl|CDD|110677 pfam01695, IstB_IS21, 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 = 30.3 bits (69), Expect = 0.44
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 122 GILLYGPPGTGKTLIARAVA 141
+LL GPPG GKT +A A+
Sbjct: 49 NLLLLGPPGVGKTHLACALG 68
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 30.8 bits (70), Expect = 0.45
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 32/133 (24%)
Query: 72 KREEEEEASNA-VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPG 130
EE+ S + I G + Q+ + +E+ + S +L+ G G
Sbjct: 208 NLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDST-----------VLIRGETG 256
Query: 131 TGKTLIARAVANETGAF---FFLINGPEIMSKLAGESE------------SNLRKA-FEE 174
TGK L+ARA+ + F +N + L ESE N R+ FE
Sbjct: 257 TGKELVARAIHQLSPRRDKPFVKLNCAALPESLL-ESELFGHEKGAFTGAINTRRGRFEL 315
Query: 175 ADKNSPSIIFIDE 187
AD + +F+DE
Sbjct: 316 ADGGT---LFLDE 325
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 30.3 bits (69), Expect = 0.48
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 118 KPPRGILLYGPPGTGKT-LIARAVANETGAFFFLINGPE 155
K +L G G+GK+ L+A+A+A + +++ PE
Sbjct: 21 KKVVRFVLTGERGSGKSVLLAQAMAYAFTQGWIVLHVPE 59
>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 = 30.2 bits (69), Expect = 0.49
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS 179
R + L+G G+GK+ + +A G + E + E +
Sbjct: 38 DRFLYLWGESGSGKSHLLQAACAA-----AEERGKSAIYLPLAELAQADPEVLEGLE--Q 90
Query: 180 PSIIFIDELDAIAPKRE 196
++ +D+++AIA + E
Sbjct: 91 ADLVCLDDVEAIAGQPE 107
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 30.1 bits (68), Expect = 0.50
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFF 148
+L G G+GK+ IA A+A+ GA F
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKF 26
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 30.3 bits (69), Expect = 0.53
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 120 PRG--ILLYGPPGTGKTLIA 137
PRG +L+ G PGTGKT+
Sbjct: 17 PRGRVVLITGGPGTGKTIFG 36
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 0.58
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 123 ILLYGPPGTGKTLIARAVAN 142
I++ G P TGKT + A+A
Sbjct: 2 IVITGGPSTGKTTLLEALAA 21
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.9 bits (68), Expect = 0.59
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 119 PPRGILLYGPPGTGKTLIARAVANETGAFFF 149
I+L G G GK+ I RA+A F
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 30.5 bits (69), Expect = 0.59
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 122 GILLYGPPGTGKTLIARAVA 141
G L+ G GT K+ +ARA+A
Sbjct: 40 GALIAGEKGTAKSTLARALA 59
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 30.7 bits (70), Expect = 0.59
Identities = 27/83 (32%), Positives = 35/83 (42%), Gaps = 25/83 (30%)
Query: 125 LYGPPGTGKTLIARAVANETGAFFFLING--PE------IMS----------KLAGESES 166
L G PG GKT I +A ++NG PE +++ K GE E
Sbjct: 199 LIGEPGVGKTAIVEGLAQR------IVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEE 252
Query: 167 NLRKAFEEADKNSPSII-FIDEL 188
L+ E K+ II FIDEL
Sbjct: 253 RLKAVLNEVTKSEGQIILFIDEL 275
>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 = 29.8 bits (68), Expect = 0.61
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 115 IGVKPPRGILLYGPPGTGKTLIARAVA 141
+KP +L+ GP GTGK+ + RA+A
Sbjct: 22 FEIKPGDRLLITGPSGTGKSSLFRALA 48
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.8 bits (68), Expect = 0.67
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 121 RGIL--LYGPPGTGKTLIA 137
RG + +YGPPG+GKT I
Sbjct: 22 RGTITQIYGPPGSGKTNIC 40
>gnl|CDD|233822 TIGR02329, propionate_PrpR, propionate catabolism operon regulatory
protein PrpR. At least five distinct pathways exists
for the catabolism of propionate by way of
propionyl-CoA. Members of this family represent the
transcriptional regulatory protein PrpR, whose gene is
found in most cases divergently transcribed from an
operon for the methylcitric acid cycle of propionate
catabolism. 2-methylcitric acid, a catabolite by this
pathway, is a coactivator of PrpR.
Length = 526
Score = 30.2 bits (68), Expect = 0.67
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 11/55 (20%)
Query: 86 DDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAV 140
DD+ G + Q++ +V L R + +L+ G GTGK L+A+A+
Sbjct: 212 DDLLGASAPMEQVRALVRLYARSDA-----------TVLILGESGTGKELVAQAI 255
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.7 bits (65), Expect = 0.70
Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 117 VKPPRGILLYGPPGTGKTLIA----RAVANETGAFFFLINGPEIMSKL 160
+ + L+ G+GKTL A +A F++ +++ +
Sbjct: 15 LLEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRKDLLEQA 62
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 30.0 bits (69), Expect = 0.74
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFF 148
P+ IL+ GP G GKT IAR +A A F
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLANAPF 78
Score = 28.1 bits (64), Expect = 3.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 182 IIFIDELDAIAPKRE 196
I+FIDE+D IA +
Sbjct: 252 IVFIDEIDKIAARGG 266
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 29.8 bits (68), Expect = 0.74
Identities = 12/18 (66%), Positives = 12/18 (66%)
Query: 124 LLYGPPGTGKTLIARAVA 141
L GP GTGKT IAR A
Sbjct: 40 LFSGPRGTGKTSIARIFA 57
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 29.8 bits (67), Expect = 0.77
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 95 LAQIKEMVEL----PLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
L ++K++ L + + V+ I + GP G GK+ + + VA+
Sbjct: 3 LLELKQVGYLAGDAKILNNISLS---VRAGEFIAITGPSGCGKSTLLKIVAS 51
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 30.0 bits (68), Expect = 0.77
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 18/81 (22%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAF--FFLIN---------GPEIMSKLAGESESNLRK- 170
+LL G GTGK ++ARA+ + A F +N E+ +AG RK
Sbjct: 339 VLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIESELFGYVAGAFTGARRKG 398
Query: 171 ---AFEEADKNSPSIIFIDEL 188
E+AD +F+DE+
Sbjct: 399 YKGKLEQADG---GTLFLDEI 416
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 29.9 bits (67), Expect = 0.78
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 123 ILLYGPPGTGKTLIARAV-----------ANETGAFFFLIN 152
+LL GPPGTGKT++A + A E+ A L+N
Sbjct: 213 LLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVN 253
>gnl|CDD|238713 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 = 29.5 bits (67), Expect = 0.86
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 123 ILLYGPPGTGKTLIARAVANETG 145
ILL GPPG+GK A +A + G
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYG 24
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 29.7 bits (67), Expect = 0.87
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 121 RGIL--LYGPPGTGKTLIARAVANET 144
RG + +YGPPG+GKT I +A
Sbjct: 11 RGTITQIYGPPGSGKTNICMILAVNA 36
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 30.2 bits (68), Expect = 0.87
Identities = 26/84 (30%), Positives = 35/84 (41%), Gaps = 25/84 (29%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLING--PEIM----------------SKLAGESE 165
+L G PG GKT I +A +ING PE + +K GE E
Sbjct: 203 VLIGEPGVGKTAIVEGLAQR------IINGEVPEGLKGRRVLALDMGALVAGAKYRGEFE 256
Query: 166 SNLRKAFEEADKNSPSII-FIDEL 188
L+ + K ++I FIDEL
Sbjct: 257 ERLKGVLNDLAKQEGNVILFIDEL 280
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 29.6 bits (67), Expect = 0.93
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 103 ELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 156
EL R LF IG K RG L+ PP GKT + +++AN N PE+
Sbjct: 1 ELSTRVVDLFAPIG-KGQRG-LIVAPPKAGKTTLLQSIANAITK-----NHPEV 47
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 29.4 bits (67), Expect = 0.96
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 127 GPPGTGKTLIARAVA 141
GP GTGKT +A A A
Sbjct: 26 GPAGTGKTYLAVAAA 40
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 29.5 bits (67), Expect = 0.96
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGA 146
P+ I++ GP +GKT +A A+A G
Sbjct: 3 PKLIVIAGPTASGKTALAIALAKRLGG 29
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 29.4 bits (66), Expect = 1.0
Identities = 17/46 (36%), Positives = 23/46 (50%)
Query: 98 IKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
IK+ E + + F+ I I L G PG+GKT + A ANE
Sbjct: 95 IKDAYECAVEYVKDFEKIQESRKNSIALLGQPGSGKTHLLTAAANE 140
>gnl|CDD|238979 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 = 28.8 bits (65), Expect = 1.0
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I++ G G+GK+ + +A+A GA F
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 27.7 bits (62), Expect = 1.1
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 117 VKPPRGILLY-GPPGTGKTLIARAVA 141
R + + G PGTGKT A A+
Sbjct: 6 AASGRSLFVVDGGPGTGKTATAAAII 31
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.8 bits (65), Expect = 1.2
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 123 ILLYGPPGTGKTLIARAVANETG 145
IL+ GPPG GK+ +A+ +A + G
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLG 25
>gnl|CDD|181180 PRK07952, PRK07952, DNA replication protein DnaC; Validated.
Length = 244
Score = 29.0 bits (65), Expect = 1.3
Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 14/71 (19%)
Query: 127 GPPGTGKTLIARAVANE---TGAFFFLINGPEIMSKLAGE------SESNLRKAFEEADK 177
G PGTGK +A A+ NE G +I +IMS + SE L D
Sbjct: 106 GKPGTGKNHLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNVD- 164
Query: 178 NSPSIIFIDEL 188
++ IDE+
Sbjct: 165 ----LLVIDEI 171
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 28.4 bits (64), Expect = 1.4
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 127 GPPGTGKTLIARAVANETGAFF 148
G G+GK+ + A+A GA F
Sbjct: 2 GVSGSGKSTVGSALAERLGAKF 23
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 29.3 bits (66), Expect = 1.4
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANETGAF 147
+KP ++ G PG+G + + + +A+ T F
Sbjct: 84 IKPGELTVVLGRPGSGCSTLLKTIASNTDGF 114
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 27.3 bits (61), Expect = 1.5
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I + G G+GK+ +A+ +A + G
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSV 28
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 29.1 bits (65), Expect = 1.5
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 123 ILLYGPPGTGKTLIARAVA---NETGAFFFLINGPEIMSKL-AGESESNLRKAFEEADK 177
+LL+GPPG GK+ +A A+ E G +++ KL E L A + DK
Sbjct: 109 LLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDK 167
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 29.2 bits (66), Expect = 1.6
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 20/81 (24%)
Query: 123 ILLYGPPGTGKTLIARAV---ANETGAFFFLINGPEIMSKLAGESE-----------SNL 168
+L+ G GTGK L+ARA+ + F +N I L ESE +
Sbjct: 167 VLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLL-ESELFGHEKGAFTGAIT 225
Query: 169 RKA--FEEADKNSPSIIFIDE 187
R+ FE+A+ +F+DE
Sbjct: 226 RRIGRFEQANG---GTLFLDE 243
>gnl|CDD|184118 PRK13531, PRK13531, regulatory ATPase RavA; Provisional.
Length = 498
Score = 28.8 bits (65), Expect = 1.7
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 123 ILLYGPPGTGKTLIAR 138
+ L GPPG K+LIAR
Sbjct: 42 VFLLGPPGIAKSLIAR 57
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 29.1 bits (65), Expect = 1.8
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 125 LYGPPGTGKTLIARAVANETG 145
L GPPG GKT + +++A TG
Sbjct: 354 LVGPPGVGKTSLGQSIAKATG 374
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 28.3 bits (64), Expect = 1.8
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 123 ILLYGPPGTGKTLIARAVANETG 145
++L GPPG+GK A+ +A + G
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYG 24
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 28.6 bits (65), Expect = 1.9
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+LL+G GTGK+ + +A+ NE
Sbjct: 56 VLLWGARGTGKSSLVKALLNE 76
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.5 bits (64), Expect = 1.9
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 123 ILLYGPPGTGKTLIARAV---ANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS 179
I+L GP G GKT +A A+ A G +++ +L+ K + +
Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMA 164
Query: 180 PSIIFIDELDAIAPKRE 196
P ++ IDE+ + +E
Sbjct: 165 PRLLIIDEIGYLPFSQE 181
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 28.1 bits (63), Expect = 2.0
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFF 149
R I L GP G GK+ I R +A + F+
Sbjct: 5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFY 33
>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc
[Central intermediary metabolism, Nitrogen metabolism,
Regulatory functions, DNA interactions, Signal
transduction, Two-component systems].
Length = 463
Score = 28.6 bits (64), Expect = 2.1
Identities = 30/96 (31%), Positives = 46/96 (47%), Gaps = 22/96 (22%)
Query: 111 LFKAIG--VKPPRGILLYGPPGTGKTLIARAVANET---GAFFFLINGPEIMSKLAGESE 165
+F+AIG + +L+ G GTGK L+ARA+ + F +N I L ESE
Sbjct: 146 VFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLI-ESE 204
Query: 166 -----------SNLRKA--FEEADKNSPSIIFIDEL 188
+N R+ FE+AD + +F+DE+
Sbjct: 205 LFGHEKGAFTGANTRRQGRFEQADGGT---LFLDEI 237
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 28.6 bits (64), Expect = 2.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 120 PRGILLYGPPGTGKTLIARAVA 141
P +LL+G G GK A+ +A
Sbjct: 21 PHALLLHGQAGIGKLDFAQHLA 42
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.6 bits (64), Expect = 2.2
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFFFLI 151
R ++ P G GKT++A E ++
Sbjct: 55 ERRGVIVLPTGAGKTVVAAEAIAELKRSTLVL 86
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 28.4 bits (64), Expect = 2.5
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 118 KPPRGIL-LYGPPGTGKTLIARAVANE 143
G++ + G G GKT +A+ + N+
Sbjct: 16 SDNLGVVGIVGMGGVGKTTLAKQIYND 42
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 27.8 bits (62), Expect = 2.6
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETG 145
+L+ G G+GKT +A A+A TG
Sbjct: 15 MITVLIDGRSGSGKTTLAGALAARTG 40
>gnl|CDD|233584 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, DNA
interactions].
Length = 534
Score = 28.5 bits (64), Expect = 2.7
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 20/87 (22%)
Query: 123 ILLYGPPGTGKTLIARAV---ANETGAFFFLINGPEIMSKLAGESE------------SN 167
+LL G GTGK LIA+A+ + F +N + L ESE
Sbjct: 222 VLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSETLL-ESELFGHEKGAFTGAIA 280
Query: 168 LRKA-FEEADKNSPSIIFIDELDAIAP 193
RK FE AD + +F+DE+ I+P
Sbjct: 281 QRKGRFELADGGT---LFLDEIGEISP 304
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 28.3 bits (64), Expect = 2.8
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+ +YG G GKT + A+ NE
Sbjct: 139 LFIYGGVGLGKTHLLHAIGNE 159
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 28.1 bits (63), Expect = 2.8
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 120 PRGILLYGPPGTGKTLIARAVA 141
P LL+GP G GK +A +A
Sbjct: 22 PHAYLLHGPAGIGKRALAERLA 43
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 28.6 bits (64), Expect = 2.9
Identities = 31/139 (22%), Positives = 44/139 (31%), Gaps = 35/139 (25%)
Query: 92 RKQLAQIKEMVEL-PLRHPSLF------KAIGVKPPRG----ILLYGPPGTGKT------ 134
R K L A+ +L+ G PG+GKT
Sbjct: 183 RIFDLNTKGEKRFDEEFLLELTQSADDQDALPGLEALEKYAKLLILGAPGSGKTTFLQRL 242
Query: 135 ---LIARAVANETGAFFFLINGPEIMSK----------LAGESESN-----LRKAFEEAD 176
L R + E F L+N + K LA E S L +A +E
Sbjct: 243 ALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDYLAEELFSQGIAKQLIEAHQELL 302
Query: 177 KNSPSIIFIDELDAIAPKR 195
K ++ +D LD + PK
Sbjct: 303 KTGKLLLLLDGLDELEPKN 321
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 28.4 bits (63), Expect = 3.0
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANETG 145
P R +L+ GP G GK+ + ++ E G
Sbjct: 107 NAPKRILLITGPSGCGKSTTIKILSKELG 135
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and
metabolism].
Length = 189
Score = 27.7 bits (62), Expect = 3.0
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE 163
K + +++ G PG GKT + + E ++N ++M ++A +
Sbjct: 2 KGRKVVVITGVPGVGKTTVLKIALKEL-VKHKIVNYGDLMLEIAKK 46
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 27.9 bits (62), Expect = 3.0
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 122 GILLYGPPGTGKTLIARAVANE 143
++ GPPG+GK IA+ ++NE
Sbjct: 2 KLVFLGPPGSGKGTIAKILSNE 23
>gnl|CDD|218872 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function. The C-terminal
half of this family contains a P-loop motif.
Length = 284
Score = 28.0 bits (63), Expect = 3.2
Identities = 16/59 (27%), Positives = 21/59 (35%), Gaps = 13/59 (22%)
Query: 92 RKQLAQIKEMVELPLRH--------PSLFKAIGVKPPRGIL-LYGPPGTGKTLIARAVA 141
R+Q+A V PL L K +G + G G TGKT + A
Sbjct: 158 RRQVA--ALCVGNPLLILAVSAALAAPLLKLLGAEG--GGFHFVGDSSTGKTTALKLAA 212
>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR;
Provisional.
Length = 441
Score = 28.1 bits (62), Expect = 3.4
Identities = 35/132 (26%), Positives = 51/132 (38%), Gaps = 34/132 (25%)
Query: 93 KQLAQIKEM-VELPLRHPSLFKAIGVKPPR---------------GILLYGPPGTGKTLI 136
K LA + E P S F +G P +L++G GTGK L+
Sbjct: 119 KALAHTHSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELV 178
Query: 137 ARAV----ANETGAFFFL----INGPEIMSKLAGESESNLRKA-------FEEADKNSPS 181
ARA+ A L +N + S+L G + A F EAD +
Sbjct: 179 ARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGT-- 236
Query: 182 IIFIDELDAIAP 193
+F+DE+ I+P
Sbjct: 237 -LFLDEIGDISP 247
>gnl|CDD|215967 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 27.9 bits (63), Expect = 3.6
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 123 ILLYGPPGTGKTL 135
+++YGPP TGK++
Sbjct: 265 LVIYGPPDTGKSM 277
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 27.6 bits (62), Expect = 4.1
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 11/65 (16%)
Query: 79 ASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIAR 138
+S ++ DD+G A I E LR + IL+ G G+GKT +
Sbjct: 99 SSRSLTLDDLGMTGAFDADIAEF----LRQAVQARGN-------ILVSGGTGSGKTTLLY 147
Query: 139 AVANE 143
A+ NE
Sbjct: 148 ALLNE 152
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 27.2 bits (61), Expect = 4.1
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFF 148
+ L G G GKT + A+A G F
Sbjct: 5 LFLVGARGCGKTTVGMALAQALGYRF 30
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 27.8 bits (62), Expect = 4.3
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANETGAFF 148
V+ R IL+ G G+GKT + A+ NE
Sbjct: 145 VRAHRNILVIGGTGSGKTTLVNAIINEMVIQD 176
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 27.8 bits (62), Expect = 4.4
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
++L GPPGTGKT A+A+E
Sbjct: 37 LILSGPPGTGKTTSILALAHE 57
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 27.2 bits (61), Expect = 4.4
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 116 GVKPPRGILLYGPPGTGKTLIARAVANET 144
G R L+G G+G++ + +A+ +
Sbjct: 38 GPVADRFFYLWGEAGSGRSHLLQALVADA 66
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 27.6 bits (62), Expect = 4.6
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 16/62 (25%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSII 183
L GP G G+ L A ++S+ G N+R+ EE N P ++
Sbjct: 30 LFAGPEGVGRKLAALCFIE------------GLLSQ--GSPSKNIRRRLEE--GNHPDLL 73
Query: 184 FI 185
++
Sbjct: 74 WV 75
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 27.8 bits (62), Expect = 4.6
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 120 PRG--ILLYGPPGTGKTLIARAVA 141
+G + L GP G GKT + R VA
Sbjct: 30 KQGTMVTLLGPSGCGKTTVLRLVA 53
>gnl|CDD|215491 PLN02906, PLN02906, xanthine dehydrogenase.
Length = 1319
Score = 27.7 bits (62), Expect = 4.7
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 17/79 (21%)
Query: 13 FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDP------------APYCIVAA 60
FE Y+K F +A+R DD+ IV GMR V+ + D + AP + A
Sbjct: 410 FE-YVKE-FKQAHR--RDDDIAIVNAGMR-VKLEEKDGEWIVSDASIAYGGVAPLSVSAR 464
Query: 61 DTVIHCEGDPIKREEEEEA 79
T G P +E ++A
Sbjct: 465 KTEEFLIGKPWNKETLQDA 483
>gnl|CDD|224586 COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 359
Score = 27.4 bits (61), Expect = 5.0
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 4/65 (6%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRK 170
L K I +PP + +YG GKT + + E + L++ +
Sbjct: 14 LLKIIESEPPSIVFIYGRRRVGKTSLLKEFIKEKLGIYILVDF----YINLRNKRFSSYL 69
Query: 171 AFEEA 175
F EA
Sbjct: 70 DFIEA 74
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 27.5 bits (61), Expect = 5.0
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
I+L G PG GK+ ++ +A +
Sbjct: 2 IILTGLPGVGKSTFSKELAKK 22
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 27.4 bits (61), Expect = 5.1
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 124 LLYGPPGTGKTLIARAVA 141
+L G PGTGKT I RA+
Sbjct: 342 ILTGGPGTGKTTITRAII 359
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.1 bits (60), Expect = 5.2
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 121 RGILLYGPPGTGKTLIA 137
R ++L P G+GKTL A
Sbjct: 25 RDVILAAPTGSGKTLAA 41
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 27.1 bits (60), Expect = 5.2
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 123 ILLYGPPGTGKTLIARAVANETG 145
+ G PG GKT I+ +A
Sbjct: 6 HFIGGIPGVGKTSISGYIARHRA 28
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 27.6 bits (62), Expect = 5.2
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 12/57 (21%)
Query: 92 RKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKT-----LIARAVANE 143
R L + M +P+R + K GV + L GP G GKT L AR
Sbjct: 200 RYLLELLANM--IPVRVEDILKQGGV-----VALVGPTGVGKTTTLAKLAARYALLY 249
>gnl|CDD|226412 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
mechanisms].
Length = 205
Score = 27.2 bits (60), Expect = 5.7
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 110 SLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFF 148
L G+ R +LL G GK+ IA A + +
Sbjct: 13 RLAAMAGMPEGRIVLLNGGSSAGKSSIALAFQDLAAEPW 51
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 27.5 bits (62), Expect = 5.8
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 123 ILLYGPPGTGKTL 135
+++YGPP TGK++
Sbjct: 437 LVIYGPPDTGKSM 449
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 27.0 bits (60), Expect = 5.9
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I + GP G GK+ +A+AVA + G +
Sbjct: 5 IAIDGPSGAGKSTVAKAVAEKLGYAYL 31
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 26.8 bits (60), Expect = 6.3
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 121 RGILLYGPPGTGKTLIARAVA 141
R ++ GP GTGKT +A
Sbjct: 19 RVAVVQGPAGTGKTTSLKAAR 39
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 27.0 bits (60), Expect = 6.8
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 118 KPPRG--ILLYGPPGTGKTLIARAVANETG 145
+PPR +L+ G G GK+++A A+A G
Sbjct: 251 RPPRPLHVLIGGVSGVGKSVLASALAYRLG 280
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 27.1 bits (60), Expect = 6.8
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVA 141
K P+ ILL G G GKT AR ++
Sbjct: 33 KIPQSILLVGASGVGKTTCARIIS 56
>gnl|CDD|180403 PRK06107, PRK06107, aspartate aminotransferase; Provisional.
Length = 402
Score = 27.0 bits (60), Expect = 7.2
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 52 PAPYCIVAADTVIHCEGDPI 71
PAPY + D V+ +G P+
Sbjct: 123 PAPYWVSYPDMVLANDGTPV 142
>gnl|CDD|221968 pfam13189, Cytidylate_kin2, Cytidylate kinase-like family. This
family includes enzymes related to cytidylate kinase.
Length = 176
Score = 26.8 bits (60), Expect = 7.2
Identities = 12/62 (19%), Positives = 24/62 (38%)
Query: 129 PGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
G+G I + +A + G ++ + +K +G SE + E+A + I
Sbjct: 8 FGSGGREIGKKLAEKLGIPYYDREILDEAAKESGISEEEFERYDEKAPNSLLYSIAAGFY 67
Query: 189 DA 190
Sbjct: 68 RG 69
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 26.8 bits (60), Expect = 7.2
Identities = 10/45 (22%), Positives = 23/45 (51%)
Query: 119 PPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE 163
+ +++ G PG GKT + + + ++N ++M ++A E
Sbjct: 1 MMKVVVVTGVPGVGKTTVLNKALEKLKEDYKIVNFGDVMLEVAKE 45
>gnl|CDD|143430 cd07112, ALDH_GABALDH-PuuC, Escherichia coli NADP+-dependent
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
PuuC-like. NADP+-dependent,
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
(GABALDH) PuuC of Escherichia coli which catalyzes the
conversion of putrescine to 4-aminobutanoate and other
similar sequences are present in this CD.
Length = 462
Score = 27.2 bits (61), Expect = 7.5
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 164 SESNLRKAFEEADKNSPSIIFID--ELDAIAPK 194
+SNL++ + E SP+I+F D +LDA A
Sbjct: 224 GQSNLKRVWLECGGKSPNIVFADAPDLDAAAEA 256
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 27.0 bits (60), Expect = 7.6
Identities = 20/50 (40%), Positives = 23/50 (46%), Gaps = 15/50 (30%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTL----IARAVANETGAFFFLINGPEI 156
L IG K RG L+ PP GKT+ IA AVA N PE+
Sbjct: 126 LVAPIG-KGQRG-LIVAPPRAGKTVLLQQIAAAVAA---------NHPEV 164
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 27.0 bits (61), Expect = 7.7
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 164 SESNLRKAFEEADKNSPSIIFID 186
+E+NL ++ P ++ ID
Sbjct: 141 AETNLEAILATIEEEKPDLVVID 163
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 27.0 bits (60), Expect = 7.7
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 103 ELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA 146
E+ S ++ G K +++ GP +GK+ + +AN+ A
Sbjct: 58 EIADTWESKSESAG-KVGV-VMVVGPVDSGKSTLTTYLANKLLA 99
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 26.8 bits (59), Expect = 7.8
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 115 IGVKPPRGILLYGPPGTGKTLIARAV 140
+ ++ ILL GP G GK+ +AR +
Sbjct: 203 VAIRSRAPILLNGPTGAGKSFLARRI 228
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB.
Length = 226
Score = 26.8 bits (60), Expect = 7.9
Identities = 7/20 (35%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 120 PRGIL--LYGPPGTGKTLIA 137
P G + ++G G+GKT +
Sbjct: 17 PTGRITEIFGEFGSGKTQLC 36
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 26.9 bits (60), Expect = 8.0
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 12/65 (18%)
Query: 123 ILLYGPPGTGKTLIARAVANET---GAFFFLIN---------GPEIMSKLAGESESNLRK 170
+LL G G GK L+A+A+ NE+ + +N E + +SE+
Sbjct: 351 VLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDRTDSENGRLS 410
Query: 171 AFEEA 175
FE A
Sbjct: 411 KFELA 415
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 26.5 bits (59), Expect = 8.2
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 123 ILLYGPPGTGKTLIARAVA 141
I + G PG GKT + + +
Sbjct: 3 IAITGTPGVGKTTVCKLLR 21
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 26.8 bits (60), Expect = 8.5
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 127 GPPGTGKTLIARAVA 141
GP GTGKT +A A A
Sbjct: 150 GPAGTGKTYLAVAKA 164
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 26.9 bits (60), Expect = 8.7
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 121 RGILLYGPPGTGKTLIARAVAN 142
+ + L GP G GK+ + +
Sbjct: 79 QILYLLGPVGGGKSSLVECLKR 100
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 26.7 bits (59), Expect = 8.8
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 123 ILLYGPPGTGKTLIARAVA 141
L+ GPP GKT + R +A
Sbjct: 140 TLIIGPPQVGKTTLLRDIA 158
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 26.9 bits (60), Expect = 8.9
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 18/76 (23%)
Query: 71 IKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGI------L 124
+ + +A A +I R+ A+ E + L L+ L R + L
Sbjct: 67 LAAPTKLKAD-AAAEAEI---RELRARFNEALAL-LKRSRLGG------RRYLYDLPWYL 115
Query: 125 LYGPPGTGKT-LIARA 139
+ GPPG+GKT L+ +
Sbjct: 116 VIGPPGSGKTTLLQNS 131
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes
the phosphorylation of adenosine 5'-phosphosulfate to
form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The
end-product PAPS is a biologically "activated" sulfate
form important for the assimilation of inorganic
sulfate.
Length = 149
Score = 26.3 bits (59), Expect = 9.0
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 123 ILLYGPPGTGKTLIARAVA 141
I L G G+GK+ IARA+
Sbjct: 2 IWLTGLSGSGKSTIARALE 20
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 26.7 bits (59), Expect = 9.3
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 123 ILLYGPPGTGKTLIARAVAN 142
I L+GP G+GKT + +A +
Sbjct: 144 IYLFGPEGSGKTHLMQAAVH 163
>gnl|CDD|183581 PRK12542, PRK12542, RNA polymerase sigma factor; Provisional.
Length = 185
Score = 26.2 bits (57), Expect = 9.3
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSII 183
+S + G +E+N+RK FE A K ++I
Sbjct: 144 ISSVMGITEANVRKQFERARKRVQNMI 170
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
component [Inorganic ion transport and metabolism].
Length = 345
Score = 26.5 bits (59), Expect = 9.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 125 LYGPPGTGKTLIARAVA 141
L GP G GK+ + R +A
Sbjct: 33 LLGPSGAGKSTLLRIIA 49
>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein
AtoC; Provisional.
Length = 457
Score = 26.7 bits (59), Expect = 9.5
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 123 ILLYGPPGTGKTLIARAV 140
+L+ G GTGK LIARA+
Sbjct: 169 VLISGESGTGKELIARAI 186
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 26.0 bits (58), Expect = 9.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
I + GPPG GKT + + V
Sbjct: 2 IFITGPPGVGKTTLVKKVIEL 22
>gnl|CDD|213179 cd00267, ABC_ATPase, 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 = 26.1 bits (58), Expect = 9.6
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 100 EMVELPLRHPSLFKAIGVKPPRG--ILLYGPPGTGKTLIARAVANET 144
E + + + + G + L GP G+GK+ + RA+A
Sbjct: 3 ENLSFRYGGRTALDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLL 49
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 26.5 bits (59), Expect = 9.8
Identities = 12/28 (42%), Positives = 12/28 (42%), Gaps = 5/28 (17%)
Query: 120 PRGILLYGPPGTGKT-----LIARAVAN 142
I L GP G GKT L AR V
Sbjct: 195 GGVIALVGPTGVGKTTTLAKLAARFVLE 222
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 26.0 bits (58), Expect = 9.8
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 129 PGTGKTLIARAVANETGAFFF 149
G GK+ I R +A G F
Sbjct: 1 MGAGKSTIGRLLAKALGLPFI 21
>gnl|CDD|215832 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 = 169
Score = 26.1 bits (58), Expect = 9.9
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 117 VKPPRGILLYGPPGTGKTLIA 137
+ + +L+ P G+GKTL
Sbjct: 11 ILSGKDVLVQAPTGSGKTLAF 31
>gnl|CDD|235331 PRK05022, PRK05022, anaerobic nitric oxide reductase transcription
regulator; Provisional.
Length = 509
Score = 26.7 bits (60), Expect = 10.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 123 ILLYGPPGTGKTLIARAV 140
+L+ G G GK L+ARA+
Sbjct: 213 VLILGETGVGKELVARAI 230
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 0.140 0.407
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,637,678
Number of extensions: 1040398
Number of successful extensions: 1694
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1664
Number of HSP's successfully gapped: 293
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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 (21.7 bits)
S2: 56 (25.3 bits)