RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14272
(194 letters)
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 88.6 bits (220), Expect = 2e-21
Identities = 52/174 (29%), Positives = 75/174 (43%), Gaps = 14/174 (8%)
Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLE 83
F FP++ Y IQ FM+ L LD K GI ESPTGTGK+LSL+C L W
Sbjct: 2 LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFP----- 56
Query: 84 KIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNE 143
E K I + TVSE IE++ EL+ Q + +S+K L E R++ +
Sbjct: 57 --ERIQKIKLIYLSRTVSE--IEKRLEELRKLMQKVEYESDEESEKQAQLLHELGREKPK 112
Query: 144 KRKKSLRNDQEVKVHALT-----YRNRMDEKNSKEKRKEEERDGLENETQELDE 192
SL + + + ++ +DE + + EN E
Sbjct: 113 VLGLSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLTASKARKYRYENPKVERCP 166
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 48.6 bits (116), Expect = 5e-07
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
FP F+ Q + + L + + E+PTGTGK+L+ + L + +
Sbjct: 10 AFP-GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG 63
>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3). All proteins in
this family for which funcitons are known are DNA-DNA
helicases that funciton in the initiation of
transcription and nucleotide excision repair as part of
the TFIIH complex. 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 = 705
Score = 47.0 bits (112), Expect = 2e-06
Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW 73
FP++ Y Q ++M++L +LD I E P+GTGK++SL+ IL +
Sbjct: 6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAY 53
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 36.1 bits (84), Expect = 0.010
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 20 EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSL 64
E S ++ + Q MK +Y L +S+ + E+ TGTGKSL
Sbjct: 247 EKLSLAMPKYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSL 291
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 32.7 bits (76), Expect = 0.097
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 115 RNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKE- 173
R +A+K+AL + + ++ + + +E+R++ +E++ RN SKE
Sbjct: 8 RENPEAVKEALAK-RGFPLDVDELLELDEERRELQTELEELQ----AERN----ALSKEI 58
Query: 174 ---KRKEEERDGLENETQELDE 192
KRK E+ + L E +EL E
Sbjct: 59 GQAKRKGEDAEALIAEVKELKE 80
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 32.7 bits (75), Expect = 0.11
Identities = 24/116 (20%), Positives = 47/116 (40%), Gaps = 13/116 (11%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDE-LIENIRK 140
++E K K+LE KN T + W+E +D ++AL+ Q+ +E I ++
Sbjct: 1108 NAELEKKEKELEKLKNTTPKDMWLE----------DLDKFEEALEEQEEVEEKEIAKEQR 1157
Query: 141 QNEKRKKSLR--NDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDESR 194
K K ++K + +K+ K + +E ++LD+
Sbjct: 1158 LKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKP 1213
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 32.4 bits (74), Expect = 0.15
Identities = 25/120 (20%), Positives = 56/120 (46%), Gaps = 9/120 (7%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
LE++++++++LE E E Q+ E ++ ++++L++AL K E +E R+
Sbjct: 732 LEQLQSRLEELEEELEELEEELEELQERLE-ELEEELESLEEALAKLKEEIEELEEKRQA 790
Query: 142 NEKRKKSLRN--------DQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDES 193
++ + L ++ + R + + + EEE + LE + EL+E
Sbjct: 791 LQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEE 850
Score = 28.1 bits (63), Expect = 3.8
Identities = 22/113 (19%), Positives = 51/113 (45%), Gaps = 7/113 (6%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
LE++E ++++ E + E +S E + +++ + + +E ++ + ++
Sbjct: 795 LEELEEELEEAERRLDALERE----LESLEQRRERLEQEIEELEEEIEELEEKLDELEEE 850
Query: 142 NEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDESR 194
E+ +K L +E +E + K EEE++ LE E +EL+
Sbjct: 851 LEELEKELEELKE---ELEELEAEKEELEDELKELEEEKEELEEELRELESEL 900
>gnl|CDD|187839 cd09708, Csf4_U, CRISPR/Cas system-associated DinG family
helicase Csf4. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
DinG family DNA helicase.
Length = 632
Score = 32.3 bits (73), Expect = 0.18
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 35 QSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
Q+ F +N +L + G+ E+ TG GK+L++I L +
Sbjct: 2 QALFYRNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERP 45
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 31.8 bits (72), Expect = 0.21
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 35 QSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
Q+ F N +L + G+ E+ TG GK+L++I L +
Sbjct: 2 QALFYLNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERP 45
>gnl|CDD|215465 PLN02863, PLN02863, UDP-glucoronosyl/UDP-glucosyl transferase
family protein.
Length = 477
Score = 30.6 bits (69), Expect = 0.49
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 2/42 (4%)
Query: 98 ETVSEDWIE-QQSFELKMRNQIDALKDALKSQKTYDELIENI 138
E+VSE+ +E +++ EL+ R +DA+K+ S K D ++++
Sbjct: 429 ESVSENQVERERAKELR-RAALDAIKERGSSVKDLDGFVKHV 469
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 30.4 bits (69), Expect = 0.61
Identities = 21/119 (17%), Positives = 50/119 (42%), Gaps = 7/119 (5%)
Query: 81 GLEKIEAKIKDLEISKNE------TVSEDWIEQQSFELKMRNQIDALKDALKSQKT-YDE 133
LE+++ ++K+ E E + E E + ++ +I+ L+ L +
Sbjct: 240 ELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISR 299
Query: 134 LIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDE 192
L + + E+ R +E++ +++DE + EE+ + L+ E + L+
Sbjct: 300 LEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEA 358
Score = 26.9 bits (60), Expect = 7.6
Identities = 20/117 (17%), Positives = 40/117 (34%), Gaps = 2/117 (1%)
Query: 77 HKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIE 136
+ L EA + E ++ E + +D +EL E
Sbjct: 809 RAELTLLNEEAANLRERLESLERRIAAT--ERRLEDLEEQIEELSEDIESLAAEIEELEE 866
Query: 137 NIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDES 193
I + + + L ++ R+ ++E + + + E +R L E +EL E
Sbjct: 867 LIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREK 923
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 30.2 bits (69), Expect = 0.79
Identities = 10/17 (58%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 55 ESPTGTGKSLS-LICGI 70
E+ TG GK+LS L+ GI
Sbjct: 55 EAGTGVGKTLSYLLAGI 71
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 29.6 bits (66), Expect = 0.83
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 135 IENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKE--EERDGLENETQELDE 192
+ +++K + K+KKSL QE A R ++E+ E+R+E +ER+ E + +E +E
Sbjct: 107 LRSVKKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREE 166
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 29.2 bits (66), Expect = 1.3
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 48 NSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKI 89
+ + PT GKSL + + ++Y LE E K+
Sbjct: 128 KNNRRLLNLPTSAGKSL-IQYLLSRYY-------LENYEGKV 161
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 1.4
Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 19/103 (18%)
Query: 106 EQQSFELKMRNQ-IDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHA----- 159
E+ EL+ + + +AL +++K +EL E K E+ K L + E +
Sbjct: 526 EELERELEQKAEEAEALLK--EAEKLKEELEEKKEKLQEEEDK-LLEEAEKEAQQAIKEA 582
Query: 160 ----------LTYRNRMDEKNSKEKRKEEERDGLENETQELDE 192
L + + K E R L ++ ++
Sbjct: 583 KKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEK 625
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 29.1 bits (66), Expect = 1.4
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 13/81 (16%)
Query: 115 RNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKE- 173
R DA+++ LK + ++ + + +E+R+K LR +E++ RN + SKE
Sbjct: 8 RENPDAVREKLKKRGGDALDVDKLLELDEERRKLLRELEELQ----AERN----ELSKEI 59
Query: 174 ----KRKEEERDGLENETQEL 190
KR E++ + L E +EL
Sbjct: 60 GRALKRGEDDAEELIAEVKEL 80
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 29.2 bits (66), Expect = 1.4
Identities = 12/84 (14%), Positives = 32/84 (38%)
Query: 83 EKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQN 142
E + K+L + + E+++ ++ +ID L + + + +E +
Sbjct: 6 EALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAAS 65
Query: 143 EKRKKSLRNDQEVKVHALTYRNRM 166
+ ++E K A +R +
Sbjct: 66 GEGGGGEEEEEEAKAEAAEFRAYL 89
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 29.3 bits (66), Expect = 1.4
Identities = 21/117 (17%), Positives = 50/117 (42%), Gaps = 10/117 (8%)
Query: 82 LEKIEAKIKDLEISKNETVSE-DWIEQQSFELKMRNQIDALKDALKS----QKTYDELIE 136
L+++ +++ L+ + SE IE + EL L DA + +K ++L +
Sbjct: 676 LQRLRERLEGLKRELSSLQSELRRIENRLDELS-----QELSDASRKIGEIEKEIEQLEQ 730
Query: 137 NIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDES 193
K E+ ++ + ++ ++ + E ++ + EE+ LE +L+
Sbjct: 731 EEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEAR 787
Score = 27.7 bits (62), Expect = 4.9
Identities = 25/116 (21%), Positives = 48/116 (41%), Gaps = 14/116 (12%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDA----LKDALKSQKTYDELIEN 137
LE++ KIKDL + V E E ++ + I L+DA + + I+
Sbjct: 274 LEELNKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDK 333
Query: 138 IRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDES 193
+ + E+ ++ + R R D+ + +EE + L E +E+D+
Sbjct: 334 LLAEIEELEREIE----------EERKRRDKLTEEYAELKEELEDLRAELEEVDKE 379
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 28.7 bits (65), Expect = 1.6
Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 120 ALKDALKSQKTYDELIENIRKQNEKRK--KSLRNDQEVKVHALTYRNRMDEKNSKEKRKE 177
++ AL++++ EL + I+K E+++ + + E K+ A+ + +E+ +EKR
Sbjct: 111 GMRKALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIE-KREEEERQIEEKRHA 169
Query: 178 EERDGLENETQEL 190
+E L+ + Q+L
Sbjct: 170 DEIAFLKKQNQQL 182
>gnl|CDD|217020 pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.
This domain is found associated with the Pfam tRNA
synthetase class II domain (pfam00587) and represents
the N-terminal domain of seryl-tRNA synthetase.
Length = 108
Score = 27.9 bits (63), Expect = 1.7
Identities = 17/76 (22%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 115 RNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEK 174
R +A+K+ L+ + ++ + + +E+R++ +E++ RN + ++ K K
Sbjct: 8 RENPEAVKEKLRKRGVDVLDVDELLELDEERRELQVELEELQ----AERNELSKEIGKAK 63
Query: 175 RKEEERDGLENETQEL 190
+K+E+ + L E +EL
Sbjct: 64 KKKEDAEALIAEVKEL 79
>gnl|CDD|238347 cd00636, TroA-like, Helical backbone metal receptor (TroA-like
domain). These proteins have been shown to function in
the ABC transport of ferric siderophores and metal ions
such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand
binding site is formed in the interface between two
globular domains linked by a single helix. Many of
these proteins also possess a low complexity region
containing a metal-binding histidine-rich motif
(repetitive HDH sequence). The TroA-like proteins
differ in their fold and ligand-binding mechanism from
the PBPI and PBPII proteins, but are structurally
similar, however, to the beta-subunit of the nitrogenase
molybdenum-iron protein MoFe. Most TroA-like proteins
are encoded by ABC-type operons and appear to function
as periplasmic components of ABC transporters in metal
ion uptake.
Length = 148
Score = 28.3 bits (63), Expect = 1.7
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 1/77 (1%)
Query: 86 EAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKR 145
EA + L V D + S E ++ I + AL ++ +ELI + + +
Sbjct: 73 EAWLDKLSKIAIPVVVVDEASELSLEN-IKESIRLIGKALGKEENAEELIAELDARLAEL 131
Query: 146 KKSLRNDQEVKVHALTY 162
+ L + KV +
Sbjct: 132 RAKLAKIPKKKVSLVVG 148
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 1.9
Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 14/122 (11%)
Query: 82 LEKIEAKIKDLE------ISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELI 135
LE +EA+I+DL + E ++E+ + + ++ + D L E +
Sbjct: 253 LETLEAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAV 312
Query: 136 ENIRKQNEKRKKSLRND--------QEVKVHALTYRNRMDEKNSKEKRKEEERDGLENET 187
E R++ E R + LR+ Q A + R D+ + + EE LE+E
Sbjct: 313 EARREELEDRDEELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREEAAELESEL 372
Query: 188 QE 189
+E
Sbjct: 373 EE 374
>gnl|CDD|235109 PRK03187, tgl, transglutaminase; Provisional.
Length = 272
Score = 28.4 bits (64), Expect = 2.3
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 81 GLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQI 118
L E +I S E S +++ SFEL +R I
Sbjct: 19 PLNAEERQILSQMASSQEVYSYRSLDELSFELNLRVNI 56
>gnl|CDD|219986 pfam08715, Viral_protease, Papain like viral protease. This family
of viral proteases are similar to the papain protease
and are required for proteolytic processing of the
replicase polyprotein. The structure of this protein has
shown it adopts a fold similar that of de-ubiquitinating
enzymes.
Length = 320
Score = 27.9 bits (62), Expect = 3.2
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 42 LYYTLDNSKFGIFESPTGTGKSLSLICGI--LKW-----YYDHKIVGLEKIEAKIK 90
Y TLD SK+GI+ S + G LKW + + + L+ ++ K K
Sbjct: 74 YYATLDASKYGIYLSALTQKWKFPQVGGFRVLKWRDNNCWVNSVCIALQYLKPKFK 129
>gnl|CDD|221283 pfam11875, DUF3395, Domain of unknown function (DUF3395). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 147 to 176 amino acids in length. This domain is
found associated with pfam00226.
Length = 144
Score = 27.3 bits (61), Expect = 3.3
Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 136 ENIRKQNEKRKKSLRNDQEVK-VHALTYRNRMDEKNSKEKRKEEERDGL 183
+K+ E++++ + + K A + + M + ++ +EEE+ GL
Sbjct: 5 AQKKKEQERQREKNKTEIAKKKQEAESAVSLMGDVVERKLTREEEKGGL 53
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 28.2 bits (63), Expect = 3.4
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 35 QSNFMKNLYYTLDNSKFGIFESPTGTGKSL 64
Q + + L +S+ + E+PTGTGK+L
Sbjct: 250 QLKLAELVLDQLTHSEKSLIEAPTGTGKTL 279
>gnl|CDD|213620 TIGR01433, CyoA, cytochrome o ubiquinol oxidase subunit II. This
enzyme catalyzes the oxidation of ubiquinol with the
concomitant reduction of molecular oxygen to water. This
acts as the terminal electron acceptor in the
respiratory chain. Subunit II is responsible for binding
and oxidation of the ubiquinone substrate. This sequence
is closely related to QoxA, which oxidizes quinol in
gram positive bacteria but which is in complex with
subunits which utilize cytochromes a in the reduction of
molecular oxygen. Slightly more distantly related is
subunit II of cytochrome c oxidase which uses cyt. c as
the oxidant [Energy metabolism, Electron transport].
Length = 226
Score = 27.5 bits (61), Expect = 3.6
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 69 GILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDW 104
G+L W HK+ + + +K + I E V+ DW
Sbjct: 92 GVLTWITTHKLDPYRPLASDVKPITI---EVVALDW 124
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 27.5 bits (61), Expect = 4.5
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 121 LKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEER 180
L+DA K + TY + + + QN + D E+ + + + E+E
Sbjct: 38 LRDAEKERDTYKQYLSKLESQNVEISNYEALDSELDELKK----EEERLLDELEELEKED 93
Query: 181 DGLENETQELDESR 194
D L+ E EL E +
Sbjct: 94 DDLDGELVELQEEK 107
>gnl|CDD|211398 cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic
translation initiation factor 5C and similar proteins.
eIF5C appears to be essential for the initiation of
protein translation; its actual function, and
specifically that of the C-terminal W2 domain, are not
well understood. The Drosophila ortholog, kra
(krasavietz) or exba (extra bases), may be involved in
translational inhibition in neural development. The
structure of this C-terminal domain resembles that of a
set of concatenated HEAT repeats.
Length = 194
Score = 27.2 bits (61), Expect = 4.6
Identities = 11/53 (20%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 103 DWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEV 155
++ +Q+ + + LK+ + ++ E+I ++ E+ KKS + EV
Sbjct: 27 EFYRKQASQEIKKELQQELKEMIAEEEPVKEIIAAVK---EQMKKSSLPEHEV 76
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 27.7 bits (62), Expect = 4.7
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 13/83 (15%)
Query: 112 LKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNS 171
++ +I + L+ E IE + K+ EK + + ++E +S
Sbjct: 168 GEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLR-------------EINEISS 214
Query: 172 KEKRKEEERDGLENETQELDESR 194
+ EE + LE E +EL+E +
Sbjct: 215 ELPELREELEKLEKEVKELEELK 237
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 27.5 bits (62), Expect = 4.9
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 56 SPTGTGKSLSLICGIL 71
SPTG+GK+L+ I+
Sbjct: 54 SPTGSGKTLAAFLAII 69
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 27.4 bits (62), Expect = 5.1
Identities = 23/129 (17%), Positives = 56/129 (43%), Gaps = 12/129 (9%)
Query: 64 LSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKD 123
++L+ G + Y+ K + EAKIK+ E + E ++ E + + K+
Sbjct: 12 VALVVGAVIGYFVRKKIA----EAKIKEAEEEAKRILEE---AKKEAEAIKKEALLEAKE 64
Query: 124 ALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGL 183
+ + E ++ E+R + + ++ + +++ +E+ E++ L
Sbjct: 65 EIHKLRN-----EFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKEL 119
Query: 184 ENETQELDE 192
E + QEL++
Sbjct: 120 EQKQQELEK 128
>gnl|CDD|190374 pfam02643, DUF192, Uncharacterized ACR, COG1430. Two structures
have been solved for members of this large (>500
members) family of bacterial proteins present mostly in
environmental bacteria and metagenomes (distant
homologues are also present in several Plasmodium
species). TOPSAN analysis for pdb:3pjy shows that there
is much similarity with the other solved structure,
pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a
homologue of Thermotoga maritima TM1668,
UniProt:Q9X1Z6., The homologue in Caulobacter
crescentus (CC1388), UniProt:Q9A8G6, is associated with
CspD, a cold shock protein (CC1387), UniProt:Q9A8G7.
However, the genomic context of UniProt:Q2GA55 is most
conserved with a putative xylose isomerase, suggesting
a possible role in extracellular sugar processing.
Saro_0821, UniProt:Q2GA57, is annotated as an
AMP-dependent synthetase and ligase. PDB:3m7a structure
corresponds to the C-terminal (27-165) fragment of the
YP_496102 (Saro_0823) protein and it is structurally
unique, as the best hits from Dali have a Z-score of
3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely
candidate for a new fold. Interestingly, many of the
top Dali hits are involved in sugar metabolism. There
are no obvious active site-like cavities on the protein
surface of 3m7a (http://www.topsan.org/Proteins/JCSG/).
Length = 104
Score = 26.4 bits (59), Expect = 5.2
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 27 FPFDAYDIQSNFMKNLYYTLD 47
F F + +MKN LD
Sbjct: 30 FVFPEPSPHTFWMKNTLIPLD 50
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 27.3 bits (61), Expect = 5.2
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 113 KMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSK 172
K++ +I ALK LK K L E I K K D E L + +K K
Sbjct: 281 KLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNE----KLDAEVKEKKKEKK 336
Query: 173 EKRKEEER 180
++ K++++
Sbjct: 337 KEEKKKKQ 344
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 27.1 bits (60), Expect = 6.6
Identities = 20/107 (18%), Positives = 40/107 (37%), Gaps = 4/107 (3%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTY----DELIEN 137
L IEA ++D E + + + M + ++ +++ Y DE
Sbjct: 339 LAGIEADLRDKEEAAGNGFEAERVHDLRSLECMLRYQSSQRELKQTEAAYCKRLDEKRLF 398
Query: 138 IRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLE 184
+ E+ ++ L +D+E R NS+ KEE + +
Sbjct: 399 EDEAEEEARQRLADDEEEVRAGDEAREEKIAANSQVIDKEEVCNLYD 445
>gnl|CDD|216292 pfam01086, Clathrin_lg_ch, Clathrin light chain.
Length = 225
Score = 27.0 bits (60), Expect = 6.7
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 102 EDWIEQQSFELKMRNQIDALKDAL---KSQKTYDELIENIRKQNEKRKKSLRNDQE 154
W E++ ++ R++ K K+QK D+ EN ++ EK K R + E
Sbjct: 115 RKWRERRDLRIEERDEASEKKKEELIEKAQKEIDDFYENYNEKKEKTKAQNRKEAE 170
>gnl|CDD|223436 COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 26.4 bits (59), Expect = 7.6
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 136 ENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEK 169
N++ +R K + E A + +++ K
Sbjct: 42 GNLKLLEARRAKLEKKAAEELAEAEALKEKLEGK 75
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 27.0 bits (60), Expect = 8.0
Identities = 26/114 (22%), Positives = 57/114 (50%), Gaps = 5/114 (4%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
LEK+E +++LE K + + E+ ++ L + L+ +T E +E +R++
Sbjct: 535 LEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRER 594
Query: 142 NEKRKKSLR--NDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDES 193
++ KK L+ ++ ++ L + E ++ + EEE LE+E ++L+
Sbjct: 595 LKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEE---LESELEKLNLQ 645
>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 = 26.4 bits (59), Expect = 8.0
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 109 SFELKMRNQIDALKDALKSQKTYDELIENI-RKQNEKRKKSLRNDQEVKVHALTYRNRM 166
ELK +A+++ L S K ++ + R+ + + +R +VK+ +T NR
Sbjct: 106 PMELKSPKFREAIEEVLSSNKP---VLAVVHRRSDSPLVERIRRRPDVKIFVVTEENRD 161
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 26.8 bits (60), Expect = 8.5
Identities = 17/73 (23%), Positives = 26/73 (35%), Gaps = 5/73 (6%)
Query: 118 IDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKE 177
+D L+ L L E +K + K + L D E + + E + E
Sbjct: 59 LDKLRSYLPKLNP---LREEKKKVSVKSLEELIKDVEEE--LEKIEKEIKELEEEISELE 113
Query: 178 EERDGLENETQEL 190
E LE E + L
Sbjct: 114 NEIKELEQEIERL 126
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 26.8 bits (60), Expect = 9.1
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 16 RPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFG 52
R EV F + D+ K L + + ++ G
Sbjct: 243 RAYTEVSILLTFDINPLDL---LAKLLIGSFNFTQMG 276
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 26.3 bits (58), Expect = 9.4
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
Q ++ L L + I +PTG+GK+L+ + L+ K
Sbjct: 10 RPYQKEAIEAL---LSGLRDVILAAPTGSGKTLAALLPALEALKRGK 53
>gnl|CDD|213266 cd03299, ABC_ModC_like, ATP-binding cassette domain similar to
the molybdate transporter. Archaeal protein closely
related to ModC. ModC is an ABC-type transporter and
the ATPase component of a molybdate transport system
that also includes the periplasmic binding protein ModA
and the membrane protein ModB. 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 = 235
Score = 26.1 bits (58), Expect = 10.0
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 38 FMKNLYYTLDNSKFGIFESPTGTGKS--LSLICGILK 72
+KN+ ++ + + PTG+GKS L I G +K
Sbjct: 14 KLKNVSLEVERGDYFVILGPTGSGKSVLLETIAGFIK 50
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
0.310 0.129 0.356
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,701,826
Number of extensions: 905823
Number of successful extensions: 1626
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1556
Number of HSP's successfully gapped: 310
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 56 (25.2 bits)