RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2946
(455 letters)
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 229 bits (586), Expect = 1e-70
Identities = 124/430 (28%), Positives = 209/430 (48%), Gaps = 31/430 (7%)
Query: 13 LKQDQELRFEV-ENAQIEIEVTSGLAEIFGVELVKSKKYLFPIGAKGAVYTWHGCSITMK 71
+ ++QE R EV E ++++ V SGLAEIFG EL + Y F K +YT+ GC + ++
Sbjct: 6 IPKNQEWRIEVNETQKLKVMVVSGLAEIFGTELANERWYAFR-NTKTFIYTFSGCKLKVE 64
Query: 72 NARKNMTYVSKETPMNYYMNVHIILEKQRSEAEQQSKRGPITMIVGPQDVGKSTLCHILL 131
A ++ YVS TPM N+H LEK+R + +GP M+VG GK++ C L+
Sbjct: 65 GA-CDLQYVSDTTPMPLIFNLHFFLEKRRMFNYE---KGPTVMVVGGSQNGKTSFCFTLI 120
Query: 132 NYAVRMPGLNRKPIFVDLDVGQGHVSVPGTIGALVIERPATIEDG-FSQLA--------- 181
+YA++ L +KP+F +LD Q PG I A+ ++ ++G + Q
Sbjct: 121 SYALK---LGKKPLFTNLDPSQPGNIFPGAISAIHVDAILDCQEGLWGQSLTSGATLLRL 177
Query: 182 --PIVYNYGHLTPNANLELYQHCVERLWKSVDERMNKDSKTNSSGMIINTCGWIKGDGFK 239
P+V+N+G N+ELY +L ++V R + SG ++T + D
Sbjct: 178 KNPLVFNFGLTEITENMELYDLQTSKLQEAVKARNHLVEDLRLSGCPVDTPSISQLDENL 237
Query: 240 C--LMACAKSLRVDNILVLDQERLYNELIRELPKSY--DVVLLPKSGGVVDRSRQFRAEA 295
K V+ ++VL ERLY+ L K + + K G V+ ++
Sbjct: 238 AAFYHTIIKRFEVNIVVVLGSERLYHSLKVIAEKLMINRIFFISKLDGFVEVEKEVGRSL 297
Query: 296 RDKRIKEYFYGSRLKPFNPHSFDIKFGEVQIYKIGAPVLPDSCMPLGVTATEFLTKVVLV 355
+ + I YFYGS +P +F++ + + + V S +PLG +TE + V
Sbjct: 298 QRRSISRYFYGSVNNELSPFTFNVDYKWLVVRIGEMYVANVSALPLG--STEKV-GCVET 354
Query: 356 QPGPSLLHHLLALSFA---TTESEILEQNIVGFVCVTHVDMLRQSLSVLCLQARPLPCSK 412
L + +LA+S A ++ + I+G+V V +V ++ L +LC R LP +
Sbjct: 355 SDVEVLQNSILAISEAREIEDQATVAGSPILGYVVVINVGAFKRKLRILCPVPRLLPSTA 414
Query: 413 LILTDIQYMD 422
LI D+++++
Sbjct: 415 LIQGDLKHVE 424
>gnl|CDD|219184 pfam06807, Clp1, Pre-mRNA cleavage complex II protein Clp1. This
family consists of several pre-mRNA cleavage complex II
Clp1 (or HeaB) proteins. Six different protein factors
are required in vitro for 3' end formation of mammalian
pre-mRNAs by endonucleolytic cleavage and
polyadenylation. Clp1 is a subunit of cleavage complex
IIA, which is required for cleavage, but not for
polyadenylation of pre-mRNA.
Length = 188
Score = 170 bits (434), Expect = 4e-51
Identities = 79/196 (40%), Positives = 121/196 (61%), Gaps = 11/196 (5%)
Query: 231 GWIKGDGFKCLMACAKSLRVDNILVLDQ-ERLYNELIRELP-KSYDVVLLPKSGGVVDRS 288
GW+KG+G + L+ ++ +++VL Q E+LY +L R L K DVV LPKSGGVV+RS
Sbjct: 1 GWVKGEGLELLLHAIRAFSPTHVVVLGQEEKLYPDLKRALKDKKVDVVELPKSGGVVERS 60
Query: 289 RQFRAEARDKRIKEYFYGSRLKPFNPHSFDIKFGEVQIYKIGAPVLPDSCMPLGVTATEF 348
+++R RD RI EYFYG+ P +PHSF +KF +V YKI PDS +P+G+ +
Sbjct: 61 KKYRRIIRDLRILEYFYGTLPMPLSPHSFLVKFSDVTPYKIP---FPDSTLPVGLHSDVD 117
Query: 349 LTKVVLVQPGPSLLHHLLALSFATTESE-ILEQNIVGFVCVTHVDMLRQSLSVLCLQARP 407
TKV +L H +LA+S+A + +E ++ N+ GF VT VD+ ++ +++L R
Sbjct: 118 PTKV-----LYALNHSVLAVSYAESLAENVICSNVAGFGVVTGVDVEKRVITILSPVPRE 172
Query: 408 LPCSKLILTDIQYMDR 423
LP L+++ I + D
Sbjct: 173 LPSKFLLVSSITFPDC 188
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 99.0 bits (247), Expect = 6e-25
Identities = 47/134 (35%), Positives = 63/134 (47%), Gaps = 23/134 (17%)
Query: 111 PITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPI-FVDLDVGQGHVSVPGTIGALVIER 169
PI ++VGP+D GK+TL LLNY R + LD GQG + PG I AL IE
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRR---GYRVAVVKHLDHGQGEIDKPGKIAALSIEE 57
Query: 170 PATIEDGF------------SQLAPIVYNYGHLTPNANLELYQHCVERLWKSVDERMNKD 217
PA +GF S+L+ +V G +P+ N +LY V+ L +
Sbjct: 58 PADGPEGFHQEEEMPLEELLSRLSYLVLFEGFKSPSENPKLYIVIVKEL-----AEIEDQ 112
Query: 218 SKTNS--SGMIINT 229
SG+IINT
Sbjct: 113 RNKEEDESGLIINT 126
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 102 bits (256), Expect = 9e-24
Identities = 65/231 (28%), Positives = 105/231 (45%), Gaps = 22/231 (9%)
Query: 95 ILEKQRSEAEQQSK---RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLDV 151
LE+ E +S+ + + M+VGP D GKSTL L N + RK +D DV
Sbjct: 55 PLEEIADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANKLL---ARGRKVAIIDADV 111
Query: 152 GQGHVSVPGTIGALVIERPATIEDGFSQLAPIVYNY-GHLTPNANLELYQHCVERLWKSV 210
GQ + PG I E P S+L P + G ++P Y V RL
Sbjct: 112 GQSEIGPPGFISLAFPESPVI---SLSELEPFTLYFVGSISPQGFPGRYIAGVARLV--- 165
Query: 211 DERMNKDSKTNSSGMIINTCGWIKGD-GFKCLMACAKSLRVDNILVLDQERLYNELIREL 269
+ K++ ++I+T GWIKG G + A +++ D I+ L++ + L+ +
Sbjct: 166 -DLAKKEADF----ILIDTDGWIKGWGGLELKRALIDAIKPDLIIALERANELSPLLEGV 220
Query: 270 PKSYDVVLLPKSGGVVDRSRQFRAEARDKRIKEYFYGSRLKPFNPHSFDIK 320
+V L V RSR+ R E R+++ + YF GS+++ + I+
Sbjct: 221 E---SIVYLKVPDAVAPRSREERKELREEKYRRYFEGSKIRTVDLDDVRIQ 268
>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 = 36.2 bits (83), Expect = 0.011
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLD 150
G + +IVGP GK+TL L I++D +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPP---GGGVIYIDGE 39
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 35.0 bits (81), Expect = 0.045
Identities = 33/152 (21%), Positives = 57/152 (37%), Gaps = 23/152 (15%)
Query: 115 IVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLDVGQGHVSVPGTIGALVIERPATIE 174
+VGP GK+T L +P L R V+LD ++ I I T+
Sbjct: 1 VVGPAGSGKTTFVGALSEI---LPLLGRSVYVVNLDPAAENLPYEADID---IRELITVA 54
Query: 175 DGFSQLAPIVYNYGHLTPNANLELYQHCVERLWKSVDERMNKDSKTNSSGMIINTCGWIK 234
D G PN L ++ L ++D + ++ + + +T G I+
Sbjct: 55 D-----VMEDDGLG---PNGAL---TVAMDFLRITLDW-LLEELEYEDDYYLFDTPGQIE 102
Query: 235 -----GDGFKCLMACAKSLRVDNILVLDQERL 261
+ + A SLR+ + ++D RL
Sbjct: 103 LFTHWESLARGVEALEASLRLGAVYLVDTRRL 134
>gnl|CDD|178930 PRK00211, PRK00211, sulfur relay protein TusC; Validated.
Length = 119
Score = 32.5 bits (75), Expect = 0.11
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 237 GFKCLMACAKSLR-----VDNILVLDQERLYNELIRELPKSYDVVL 277
+ CA SLR + VLD E L +R +YDVVL
Sbjct: 72 DIEQCYLCAASLRERGLDPNTDFVLDVEPLDAAALRRKLDNYDVVL 117
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 33.2 bits (77), Expect = 0.15
Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 29/97 (29%)
Query: 68 ITMKNARKNMTYVSKETPMNYYM-NVHIILEKQRSEAEQQSKRGPITMIVGPQDVGKSTL 126
I++++A + T+ S E ++ + ++++ + +G + IVGP GKS+L
Sbjct: 1 ISVEDA--SFTWDSGEQETSFTLKDINLEV-----------PKGELVAIVGPVGSGKSSL 47
Query: 127 CHILLNYAVRMPGLNRKPIFVDLDVGQGHVSVPGTIG 163
LL +L+ G VSVPG+I
Sbjct: 48 LSALLG---------------ELEKLSGSVSVPGSIA 69
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 33.0 bits (76), Expect = 0.18
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 104 EQQSKRGPITMIVGPQDVGKSTLCHILLNYAVRM---PGLNRKPIFVDL 149
E + R P + VG +VGKSTL L VR+ PG+ RKP D
Sbjct: 3 ETRPDRKPEIVFVGRSNVGKSTLVRELTGKKVRVGKRPGVTRKPNHYDW 51
>gnl|CDD|213235 cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain of
the bacitracin-resistance transporter. The BcrA
subfamily represents ABC transporters involved in
peptide antibiotic resistance. Bacitracin is a
dodecapeptide antibiotic produced by B. licheniformis
and B. subtilis. The synthesis of bacitracin is
non-ribosomally catalyzed by a multi-enzyme complex
BcrABC. Bacitracin has potent antibiotic activity
against gram-positive bacteria. The inhibition of
peptidoglycan biosynthesis is the best characterized
bacterial effect of bacitracin. The bacitracin
resistance of B. licheniformis is mediated by the ABC
transporter Bcr which is composed of two identical BcrA
ATP-binding subunits and one each of the integral
membrane proteins, BcrB and BcrC. B. subtilis cells
carrying bcr genes on high-copy number plasmids develop
collateral detergent sensitivity, a similar phenomenon
in human cells with overexpressed multi-drug resistance
P-glycoprotein.
Length = 208
Score = 32.6 bits (75), Expect = 0.28
Identities = 38/130 (29%), Positives = 50/130 (38%), Gaps = 34/130 (26%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKP---IFVDLDVGQGHVSVPGTIGA 164
K+G I +GP GK+T I+L GL + I D Q ++ IGA
Sbjct: 24 KKGEIYGFLGPNGAGKTTTMKIIL-------GLIKPDSGEITFDGKSYQKNIEALRRIGA 76
Query: 165 LVIERPATIEDGFSQLAPIVYNYGHLTPNANLELYQHCVERLWKSVDERMN--------- 215
L IE P GF Y +LT NL L + K +DE ++
Sbjct: 77 L-IEAP-----GF---------YPNLTARENLRLLARLLGIRKKRIDEVLDVVGLKDSAK 121
Query: 216 KDSKTNSSGM 225
K K S GM
Sbjct: 122 KKVKGFSLGM 131
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 32.0 bits (74), Expect = 0.47
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 107 SKRGPITMIVGPQDVGKSTLCHILLN 132
+RG + ++ GP GKSTL LL
Sbjct: 2 MRRGLLIVLSGPSGAGKSTLVKALLE 27
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 31.6 bits (71), Expect = 0.61
Identities = 32/198 (16%), Positives = 64/198 (32%), Gaps = 11/198 (5%)
Query: 112 ITMIVGPQDVGKSTLCHIL--LNYAVRMPGLNRKPIFVDLDVGQGHVSVPGTIGALVIER 169
+ +I+GP GKS L L L + + + + V + + +P + IE
Sbjct: 1 LNVIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGLNVGIKL------LPFLLDENEIEI 54
Query: 170 PATIEDGFSQLAPIVYNYGHLTPNANLELYQHCVERLWKSVDERMNKDSKTNSSGMIINT 229
P E + I Y YG + E + ++ +E + + ++ S
Sbjct: 55 PLEFEIEEFLIDGIRYRYGF---ELDKEDILEELLYEYRKGEELLFERERSKESFEKSPE 111
Query: 230 CGWIKGDGFKCLMACAKSLRVDNILVLDQERLYNELIRELPKSYDVVLLPKSGGVVDRSR 289
+ L+ SL +L + L L L ++D +
Sbjct: 112 KKRELRGLREVLLLLNLSLSSFLLLASLEILLSILLPFSFILGNLRNLRNIELKLLDLVK 171
Query: 290 QFRAEARDKRIKEYFYGS 307
+ E+ R+ +
Sbjct: 172 RLFLESDLLRLLKLLIKG 189
>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 = 31.3 bits (71), Expect = 0.63
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 112 ITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLD 150
+ ++ GP GK+TL L G K ++VD++
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGG---KVVYVDIE 36
>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 = 31.6 bits (72), Expect = 0.64
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVD 148
RG IT I GP GK+ +C IL AV +K +++D
Sbjct: 11 RGTITQIYGPPGSGKTNICMIL---AVNAARQGKKVVYID 47
>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 = 31.4 bits (72), Expect = 0.64
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 109 RGPITMIVGPQDVGKSTLCHIL-LN--YAVRMPGLNRKPIFVD 148
G IT I G GK+ LC L + + GL K +++D
Sbjct: 18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID 60
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 31.0 bits (71), Expect = 0.81
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 112 ITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLD 150
+ ++VG Q GK+T L Y + +K + V D
Sbjct: 3 VILLVGLQGSGKTTTIAKLAAYLKKQ---GKKVLLVAAD 38
>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 = 30.3 bits (69), Expect = 1.0
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLDVGQGHV 156
RG +T++ G GKSTL L+ A + +P V G V
Sbjct: 32 RGGLTLLAGAPGTGKSTL---ALDLAAAV--ATGRPFLGPFPVEPGRV 74
>gnl|CDD|213215 cd03248, ABCC_TAP, ATP-binding cassette domain of the Transporter
Associated with Antigen Processing, subfamily C. TAP
(Transporter Associated with Antigen Processing) is
essential for peptide delivery from the cytosol into the
lumen of the endoplasmic reticulum (ER), where these
peptides are loaded on major histocompatibility complex
(MHC) I molecules. Loaded MHC I leave the ER and display
their antigenic cargo on the cell surface to cytotoxic T
cells. Subsequently, virus-infected or malignantly
transformed cells can be eliminated. TAP belongs to the
large family of ATP-binding cassette (ABC) transporters,
which translocate a vast variety of solutes across
membranes.
Length = 226
Score = 30.9 bits (70), Expect = 1.0
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 110 GPITMIVGPQDVGKSTLCHILLNYAVRMPG---LNRKPI 145
G +T +VGP GKST+ +L N+ G L+ KPI
Sbjct: 40 GEVTALVGPSGSGKSTVVALLENFYQPQGGQVLLDGKPI 78
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 31.6 bits (72), Expect = 1.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 287 RSRQFRAEARDKRIK 301
R FR EA+ KRIK
Sbjct: 210 RELLFREEAKAKRIK 224
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 31.1 bits (71), Expect = 1.1
Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 6/62 (9%)
Query: 85 PMNYYMNVHIILEKQRSEAE---QQSKRGPITMIV---GPQDVGKSTLCHILLNYAVRMP 138
P++ + +++ ++ + I+ G VGKST IL R P
Sbjct: 51 PLSRLLQLYVEARERLFAELLRFLGTNNQQRPFIIGIAGSVAVGKSTTARILQALLSRWP 110
Query: 139 GL 140
Sbjct: 111 ES 112
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea, these
transporters usually include an ATP-binding protein and
one or two integral membrane proteins. Eukaryotic
systems of the ABCA subfamily display ABC domains that
are quite similar to this family. The ATP-binding domain
shows the highest similarity between all members of the
ABC transporter 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 = 173
Score = 30.4 bits (70), Expect = 1.1
Identities = 26/96 (27%), Positives = 37/96 (38%), Gaps = 28/96 (29%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKP----IFVD-LDVGQGHVSVPGTI 162
++G I ++GP GK+TL I+L KP I V D+ + V I
Sbjct: 24 EKGEIYGLLGPNGAGKTTLIKIILGL--------LKPDSGEIKVLGKDIKKEPEEVKRRI 75
Query: 163 GALVIERPATIEDGFSQLAPIVYNYGHLTPNANLEL 198
G L E+ Y +LT NL+L
Sbjct: 76 GYL-------PEE--------PSLYENLTVRENLKL 96
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 30.6 bits (70), Expect = 1.2
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 107 SKRGPITMIVGPQDVGKSTLCHILLN 132
+G + ++ GP VGKSTL LL
Sbjct: 1 MSKGLLIVLSGPSGVGKSTLVKALLE 26
>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 = 29.4 bits (67), Expect = 1.4
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 110 GPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLD 150
I +I GP+ VGK+TL LL + + L+ ++++LD
Sbjct: 2 NKIIVITGPRQVGKTTL---LLQFLKEL--LSENILYINLD 37
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 30.2 bits (69), Expect = 1.7
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVD 148
RG IT I GP GK+ +C L A + +K I++D
Sbjct: 22 RGTITQIYGPPGSGKTNICLQLAVEAAK---NGKKVIYID 58
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 30.2 bits (69), Expect = 1.9
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
+ G IVGP GKSTL ++L
Sbjct: 29 EAGEFVAIVGPSGSGKSTLLNLL 51
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 29.7 bits (68), Expect = 2.2
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
K+G +IVGP GKSTL +L
Sbjct: 25 KKGEFVLIVGPNGSGKSTLLRLL 47
>gnl|CDD|213222 cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the
transporters involved in export of lipoprotein and
macrolide, and cell division protein. This family is
comprised of MJ0796 ATP-binding cassette,
macrolide-specific ABC-type efflux carrier (MacAB), and
proteins involved in cell division (FtsE), and release
of lipoproteins from the cytoplasmic membrane (LolCDE).
They are clustered together phylogenetically. MacAB is
an exporter that confers resistance to macrolides, while
the LolCDE system is not a transporter at all. An FtsE
null mutants showed filamentous growth and appeared
viable on high salt medium only, indicating a role for
FtsE in cell division and/or salt transport. The LolCDE
complex catalyzes the release of lipoproteins from the
cytoplasmic membrane prior to their targeting to the
outer membrane.
Length = 218
Score = 29.8 bits (68), Expect = 2.4
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
++G IVGP GKSTL +IL
Sbjct: 28 EKGEFVAIVGPSGSGKSTLLNIL 50
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They belong
to the subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional spectrum
that includes ion transport, cell surface receptor, and
toxin secretion activities. The MRP-like family, similar
to all ABC proteins, have a common four-domain core
structure constituted by two membrane-spanning domains,
each composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). 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 = 171
Score = 29.3 bits (67), Expect = 2.6
Identities = 13/26 (50%), Positives = 14/26 (53%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNY 133
K G IVGP GKSTL +LL
Sbjct: 26 KPGEKVAIVGPSGSGKSTLLKLLLRL 51
>gnl|CDD|99745 cd06452, SepCysS, Sep-tRNA:Cys-tRNA synthase. This family belongs
to the pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Cys-tRNA(Cys) is
produced by O-phosphoseryl-tRNA synthetase which ligates
O-phosphoserine (Sep) to tRNA(Cys), and
Sep-tRNA:Cys-tRNA synthase (SepCysS) converts
Sep-tRNA(Cys) to Cys-tRNA(Cys), in methanogenic archaea.
SepCysS forms a dimer, each monomer is composed of a
large and small domain; the larger, a typical pyridoxal
5'-phosphate (PLP)-dependent-like enzyme fold. In the
active site of each monomer, PLP is covalently bound to
a conserved Lys residue near the dimer interface.
Length = 361
Score = 30.1 bits (68), Expect = 2.7
Identities = 35/141 (24%), Positives = 54/141 (38%), Gaps = 28/141 (19%)
Query: 76 NMTYVSKETPMNYYMNVHIILEKQRSEAEQQSKRGPITMIVGPQ-------DVGK-STLC 127
N+ V Y++ E ++ K + ++ D K + +C
Sbjct: 106 NVREVPNTGHPEYHITPEGYAEVIEEVKDEFGKPPALALLTHVDGNYGNLHDAKKIAKVC 165
Query: 128 H-----ILLN--YAV-RMPGLNRKPIFVDLDVGQGHVSV--PGTIGALVIERPATIEDGF 177
H +LLN Y V RMP ++ K + D VG GH S+ IG L AT E
Sbjct: 166 HEYGVPLLLNGAYTVGRMP-VSGKELGADFIVGSGHKSMAASAPIGVL-----ATTE--- 216
Query: 178 SQLAPIVYNYGHLTPNANLEL 198
+ A IV+ + +EL
Sbjct: 217 -EWADIVFRTSQMFKIKEVEL 236
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 29.6 bits (67), Expect = 3.0
Identities = 37/136 (27%), Positives = 52/136 (38%), Gaps = 41/136 (30%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKP----IFVD-LDVGQGHVSVPGTI 162
+ G I ++GP GK+TL IL GL KP I V DV + V I
Sbjct: 29 EPGEIFGLLGPNGAGKTTLLKILA-------GL-LKPTSGEILVLGYDVVKEPAKVRRRI 80
Query: 163 GALVIERPATIEDGFSQLAPIVYNYGHLTPNANLELY-----------QHCVERLWKSV- 210
G V + P+ Y LT NLE + + +E L +
Sbjct: 81 G-YVPQEPSL--------------YPELTVRENLEFFARLYGLSKEEAEERIEELLELFG 125
Query: 211 -DERMNKDSKTNSSGM 225
+++ NK +T S GM
Sbjct: 126 LEDKANKKVRTLSGGM 141
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 29.3 bits (66), Expect = 3.1
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 109 RGPITMIVGPQDVGKSTL 126
R PIT I G GKSTL
Sbjct: 36 RAPITFITGENGSGKSTL 53
>gnl|CDD|215376 PLN02699, PLN02699, Bifunctional molybdopterin
adenylyltransferase/molybdopterin molybdenumtransferase.
Length = 659
Score = 29.8 bits (67), Expect = 3.2
Identities = 28/89 (31%), Positives = 37/89 (41%), Gaps = 8/89 (8%)
Query: 257 DQERLYNELIRELPKSYDVVLLPKSGGVVDRSRQFRAEARDKRIKEYFYGSRLKPFNPHS 316
D+E L L + D++L SGGV R F +KR YF +KP P +
Sbjct: 234 DEEELERILDEAISSGVDILLT--SGGVSMGDRDFVKPLLEKRGTVYFSKVLMKPGKPLT 291
Query: 317 F---DIKFGEVQIYKI---GAPVLPDSCM 339
F D K K+ G P P SC+
Sbjct: 292 FAEIDAKSAPSNSKKMLAFGLPGNPVSCL 320
>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 = 28.7 bits (64), Expect = 3.5
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 106 QSKRGPITMIVGPQDVGKSTLCHILLNYAVRM 137
+ ++ GP GK+TL + N R
Sbjct: 15 ELPPPKNLLLYGPPGTGKTTLARAIANELFRP 46
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.1 bits (66), Expect = 3.7
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
++G +++GP GKSTL +L
Sbjct: 28 EKGERVLLIGPNGSGKSTLLKLL 50
>gnl|CDD|131266 TIGR02211, LolD_lipo_ex, lipoprotein releasing system, ATP-binding
protein. This model represents LolD, a member of the
ABC transporter family (pfam00005). LolD is involved in
localization of lipoproteins in some bacteria. It works
with a transmembrane protein LolC, which in some species
is a paralogous pair LolC and LolE. Depending on whether
the residue immediately following the new, modified
N-terminal Cys residue, the nascent lipoprotein may be
carried further by LolA and LolB to the outer membrane,
or remain at the inner membrane. The top scoring
proteins excluded by this model include homologs from
the archaeal genus Methanosarcina [Protein fate, Protein
and peptide secretion and trafficking].
Length = 221
Score = 29.2 bits (66), Expect = 3.7
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 109 RGPITMIVGPQDVGKSTLCHIL 130
+G I IVG GKSTL H+L
Sbjct: 30 KGEIVAIVGSSGSGKSTLLHLL 51
>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 = 29.0 bits (65), Expect = 4.3
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVD 148
RG +T + GP GK+ + + AV G +K ++D
Sbjct: 18 RGTVTQVYGPPGTGKTNIA---IQLAVETAGQGKKVAYID 54
>gnl|CDD|187793 cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily
protein Csm5. 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;
RAMP superfamily protein.
Length = 365
Score = 29.4 bits (66), Expect = 4.8
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 251 DNILVLDQERLYNELIRELPKSY 273
D I V+D E+LY +L+ + K
Sbjct: 29 DRIYVIDFEKLYADLLEKKRKDE 51
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 28.6 bits (65), Expect = 4.9
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNY 133
+ G I I+GP GKSTL L
Sbjct: 23 EAGEIVGILGPNGAGKSTLLKTLAGL 48
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 29.0 bits (66), Expect = 5.5
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
K G +T I+GP +GK+T IL
Sbjct: 97 KEGKVTGILGPNGIGKTTAVKIL 119
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 28.2 bits (64), Expect = 5.6
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 115 IVGPQDVGKSTLCHILLN 132
+VG GKSTL ++
Sbjct: 31 LVGRNGAGKSTLLKLIAG 48
>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 = 28.4 bits (64), Expect = 5.7
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLN 132
K G I +VGP GKSTL +
Sbjct: 23 KAGEIVALVGPNGSGKSTLLRAIAG 47
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.5 bits (64), Expect = 5.7
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNYAVR 136
P +I G D GK++L +L V+
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVK 29
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 28.8 bits (65), Expect = 6.2
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 109 RGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVD 148
RG IT I GP+ GK+TL L+ A + G K F+D
Sbjct: 59 RGRITEIYGPESSGKTTLALQLVANAQKPGG---KAAFID 95
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. 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 = 234
Score = 28.4 bits (64), Expect = 6.3
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 13/46 (28%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLDVGQ 153
G +VGP GKSTL +++ P F D+D G+
Sbjct: 26 PAGETVALVGPSGSGKSTLVNLI-------------PRFYDVDSGR 58
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
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 = 220
Score = 28.6 bits (65), Expect = 6.4
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
+ G +VGP GKSTL I+
Sbjct: 28 EEGEFVALVGPSGCGKSTLLRII 50
>gnl|CDD|236997 PRK11831, PRK11831, putative ABC transporter ATP-binding protein
YrbF; Provisional.
Length = 269
Score = 28.6 bits (64), Expect = 6.5
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 109 RGPITMIVGPQDVGKSTL 126
RG IT I+GP +GK+TL
Sbjct: 32 RGKITAIMGPSGIGKTTL 49
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 28.8 bits (65), Expect = 6.7
Identities = 22/87 (25%), Positives = 32/87 (36%), Gaps = 22/87 (25%)
Query: 95 ILEKQRSEAEQQSKRGPITMIVGPQDVGKSTLCHILLNYAVRMPGLNRKPIFVDLDVGQG 154
IL + + K + ++VG Q GK+T C L Y + +K + V D
Sbjct: 84 ILGGENASLNLAKKPPTVILMVGLQGSGKTTTCGKLAYYLKKK--QGKKVLLVACD---- 137
Query: 155 HVSVPGTIGALVIERPATIEDGFSQLA 181
+ RPA IE QL
Sbjct: 138 ------------LYRPAAIE----QLK 148
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP [Purines, pyrimidines, nucleosides,
and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 28.2 bits (64), Expect = 6.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 112 ITMIVGPQDVGKSTLCHILL 131
+ +I GP GKSTL LL
Sbjct: 2 LIVISGPSGAGKSTLVKALL 21
>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 = 28.1 bits (63), Expect = 7.3
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 109 RGPITMIVGPQDVGKST-LCHILLNYAVRMPGLNRKPIFVDLDVGQGHVS 157
G +T+I GP GKST L I L R+ V G +
Sbjct: 20 EGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRR-----SGVKAGCIV 64
>gnl|CDD|233665 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the SUF
system, shown in E. coli to consist of six proteins and
believed to act in Fe-S cluster formation during
oxidative stress. SufC forms a complex with SufB and
SufD. SufC belongs to the ATP-binding cassette
transporter family (pfam00005) but is no longer thought
to be part of a transporter. The complex is reported as
cytosolic (PMID:12554644) or associated with the
membrane (PMID:11943156). The SUF system also includes a
cysteine desulfurase (SufS, enhanced by SufE) and a
probable iron-sulfur cluster assembly scaffold protein,
SufA [Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 243
Score = 28.4 bits (64), Expect = 7.5
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
K+G I I+GP GKSTL +
Sbjct: 24 KKGEIHAIMGPNGSGKSTLSKTI 46
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 28.0 bits (63), Expect = 7.6
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 114 MIVGPQDVGKSTLCHILL 131
+VG +VGKSTL + LL
Sbjct: 129 YVVGATNVGKSTLINALL 146
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 28.3 bits (64), Expect = 8.0
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 110 GPITMIVGPQDVGKSTLCHIL-LN--YAVRMPGLNRKPIFVD 148
G IT I G GK+ LCH L + + + GL K +++D
Sbjct: 19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID 60
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 28.1 bits (63), Expect = 8.3
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 112 ITMIVGPQDVGKSTLCHIL 130
+ ++ G Q GKST L
Sbjct: 54 VLILQGAQGSGKSTFLKKL 72
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 28.3 bits (64), Expect = 8.6
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 11/50 (22%)
Query: 104 EQQSKRGPITMIVGPQDVGKSTLCHIL-LNYAVRMP----GLNRKPIFVD 148
E QS IT G GK+ +CH L +N V++P GL K +++D
Sbjct: 100 ETQS----ITEFYGEFGSGKTQICHQLAVN--VQLPEEKGGLEGKAVYID 143
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette transport
system involved in resistant to organic solvents. 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 = 28.2 bits (64), Expect = 8.7
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 108 KRGPITMIVGPQDVGKSTL 126
+RG I I+GP GKSTL
Sbjct: 24 RRGEILAIIGPSGSGKSTL 42
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 28.3 bits (64), Expect = 8.7
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 108 KRGPITMIVGPQDVGKSTLCHILLNY 133
+G IT I+GP GKSTL L
Sbjct: 26 PKGEITGILGPNGSGKSTLLKCLAGL 51
>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 = 26.8 bits (60), Expect = 8.7
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 114 MIVGPQDVGKSTLCHILLNYAVRMPGLNRKP 144
+ GP GKSTL L ++ GL +K
Sbjct: 2 WLYGPPGCGKSTLAKYLARALLKHLGLPKKD 32
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.3 bits (64), Expect = 8.9
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 95 ILEKQRSEAEQQS--KRGPITMIVGPQDVGKSTLCHILLNY 133
L++ + A+Q + G +I+G +VGKS+L + LL
Sbjct: 200 ELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGR 240
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the ATP-binding
cassette component of cobalt transport system. Domain
II of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. The CbiMNQO family ABC
transport system is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 205
Score = 27.6 bits (62), Expect = 9.9
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
G I + G GK+TL IL
Sbjct: 24 YAGEIIALTGKNGAGKTTLAKIL 46
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent) systems
that are largely represented in archaea and eubacteria
and are primarily involved in scavenging solutes from
the environment. 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 = 178
Score = 27.5 bits (62), Expect = 9.9
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 108 KRGPITMIVGPQDVGKSTLCHIL 130
+ G I ++GP GKSTL +
Sbjct: 24 EAGEIVALLGPSGSGKSTLLRCI 46
>gnl|CDD|226963 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 252
Score = 28.0 bits (63), Expect = 10.0
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 110 GPITMIVGPQDVGKSTL 126
G IT I+GP GKSTL
Sbjct: 27 GGITSIIGPNGAGKSTL 43
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
0.321 0.137 0.410
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,103,324
Number of extensions: 2242088
Number of successful extensions: 2347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2326
Number of HSP's successfully gapped: 95
Length of query: 455
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 355
Effective length of database: 6,502,202
Effective search space: 2308281710
Effective search space used: 2308281710
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.3 bits)