RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12149
(243 letters)
>gnl|CDD|201987 pfam01813, ATP-synt_D, ATP synthase subunit D. This is a family of
subunit D form various ATP synthases including V-type H+
transporting and Na+ dependent. Subunit D is suggested
to be an integral part of the catalytic sector of the
V-ATPase.
Length = 191
Score = 205 bits (524), Expect = 3e-67
Identities = 80/189 (42%), Positives = 115/189 (60%), Gaps = 1/189 (0%)
Query: 18 LMKSRLKGAQKGHSLLKKKADALQMRFRMILSKIIETKTLMGEVMKEAAFSLAEAKFTTG 77
+K RLK AQ+GH LLKKK DAL FR +L + E + + E +KEA FSLA A G
Sbjct: 4 RLKRRLKLAQRGHKLLKKKRDALIREFRALLREAKELREELEEALKEAYFSLALANAAEG 63
Query: 78 DFNQVVLQNVTKAQIKIRTKKDNVAGVTLPVFESYQDGTDTYELAGLARGGQQLAKLKKN 137
+ K ++++ N+ GV +PVFE + T GL L + ++
Sbjct: 64 IDFVESVAESVKRVVEVKVSTRNIMGVKVPVFELVEVETAER-PYGLLSTSAWLDEAREK 122
Query: 138 YQTAIKLLVELASLQTSFVTLDDVIKITNRRVNAIEHVIIPRIEKTLAYIISELDELERE 197
++ A++LL+ELA L+T+ L + I+ T RRVNA+E V+IPR+E+T+ YI EL+E ERE
Sbjct: 123 FEEALELLIELAELETALRLLAEEIRKTQRRVNALEKVVIPRLEETIKYIRMELEERERE 182
Query: 198 EFYRLKKIQ 206
EF+RLKKI+
Sbjct: 183 EFFRLKKIK 191
>gnl|CDD|129409 TIGR00309, V_ATPase_subD, H(+)-transporting ATP synthase, vacuolar
type, subunit D. Although this ATPase can run
backwards, using a proton gradient to synthesize ATP,
the primary biological role is to acidify some
compartment, such as yeast vacuole (a lysosomal homolog)
or the interior of a prokaryote [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 209
Score = 167 bits (424), Expect = 6e-52
Identities = 82/203 (40%), Positives = 123/203 (60%), Gaps = 2/203 (0%)
Query: 9 IFPSRGAQSLMKSRLKGAQKGHSLLKKKADALQMRFRMILSKIIETKTLMGEVMKEAAFS 68
+ P+R +K +LK A++G+SLLK K DAL M FR IL + + K M + +KEA
Sbjct: 4 VNPTRMELLKLKDKLKMAKRGYSLLKLKRDALIMEFRQILERAKDIKNKMEQKLKEAISD 63
Query: 69 LAEAKFTTGDF-NQVVLQNVTKAQIKIRTKKDNVAGVTLPVFESYQ-DGTDTYELAGLAR 126
L EA+ G F + +V A+ ++ K N+ GV +PVF+SY+ GL
Sbjct: 64 LIEAQSVMGPFAVWIAALSVVTARFEVDMKSKNIMGVVVPVFDSYEIRRKVHERGYGLLF 123
Query: 127 GGQQLAKLKKNYQTAIKLLVELASLQTSFVTLDDVIKITNRRVNAIEHVIIPRIEKTLAY 186
++ + + Y+ A++L+VELA ++T+ L + I+IT RRVNA+EHVIIPR++ T+ Y
Sbjct: 124 TSYKVDEAAEIYEEAVELIVELAEIETTIRLLAEEIEITKRRVNALEHVIIPRLKNTIKY 183
Query: 187 IISELDELEREEFYRLKKIQDKK 209
I LDE++RE F RLKKI+ K
Sbjct: 184 INMRLDEMDRENFVRLKKIKSSK 206
>gnl|CDD|224312 COG1394, NtpD, Archaeal/vacuolar-type H+-ATPase subunit D [Energy
production and conversion].
Length = 211
Score = 165 bits (419), Expect = 4e-51
Identities = 79/205 (38%), Positives = 121/205 (59%), Gaps = 1/205 (0%)
Query: 5 ERLPIFPSRGAQSLMKSRLKGAQKGHSLLKKKADALQMRFRMILSKIIETKTLMGEVMKE 64
L + P+R +K RLK A++GH LLK K DAL M FR I+ + E + + + ++E
Sbjct: 1 MSLQVKPTRMELIRLKRRLKLARRGHKLLKLKRDALIMEFRAIVKEAKELREELEKELEE 60
Query: 65 AAFSLAEAKFTTGDFNQVVLQNVTKAQIKIRTKKDNVAGVTLPVFESYQDGTDTYELAGL 124
A SLA A G + V K ++++ +N+ GV +P FE + Y+L G+
Sbjct: 61 AYESLALASAAEGIDAVEEIALVQKEKLEVDVDVENIMGVVVPTFELVELTPPPYDL-GI 119
Query: 125 ARGGQQLAKLKKNYQTAIKLLVELASLQTSFVTLDDVIKITNRRVNAIEHVIIPRIEKTL 184
L + + ++ ++ L+ELA L+T+ L + I+ T RRVNA+E+VIIPR+E T+
Sbjct: 120 LSTSAWLDEAIEKFEELLEKLIELAELETTLRLLLEEIRKTKRRVNALEYVIIPRLENTI 179
Query: 185 AYIISELDELEREEFYRLKKIQDKK 209
YI S+L+E ERE+F RLKKI+ KK
Sbjct: 180 KYIESKLEEREREDFVRLKKIKKKK 204
>gnl|CDD|178991 PRK00373, PRK00373, V-type ATP synthase subunit D; Reviewed.
Length = 204
Score = 112 bits (283), Expect = 8e-31
Identities = 66/189 (34%), Positives = 102/189 (53%)
Query: 19 MKSRLKGAQKGHSLLKKKADALQMRFRMILSKIIETKTLMGEVMKEAAFSLAEAKFTTGD 78
+K RLK A++GH LLK K D L M F IL + + + + E ++EA A+ G
Sbjct: 16 LKRRLKLAERGHKLLKDKRDELIMEFFDILDEAKKLREEVEEELEEAYKDFLMARAVEGS 75
Query: 79 FNQVVLQNVTKAQIKIRTKKDNVAGVTLPVFESYQDGTDTYELAGLARGGQQLAKLKKNY 138
K +++ N+ GV +PV E T G +L + + +
Sbjct: 76 LAVEEAAASPKESLEVDVSSKNIMGVVVPVIELSVKRTLPERGYGFLGTSAELDEAAEKF 135
Query: 139 QTAIKLLVELASLQTSFVTLDDVIKITNRRVNAIEHVIIPRIEKTLAYIISELDELEREE 198
+ ++ ++ELA ++ + L D I+ T RRVNA+E+VIIPR+E+T+ YI +LDE+ERE
Sbjct: 136 EELLEKILELAEVEKTIQLLADEIEKTKRRVNALEYVIIPRLEETIKYIKMKLDEMEREN 195
Query: 199 FYRLKKIQD 207
F RLKKI+
Sbjct: 196 FVRLKKIKS 204
>gnl|CDD|164919 PHA02458, A, protein A*; Reviewed.
Length = 341
Score = 30.6 bits (69), Expect = 0.67
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 19 MKSRLKGAQKGHSLLKKKADALQMR-FRMILSKIIETKTL-MGEVMKEAAFSLAEAKFTT 76
M ++ G ++ ++ LK K L + FR+ +S+ K L M + E L + +
Sbjct: 184 MAAKGLGNKEWNNSLKTKMALLPKKLFRIRMSRNFGMKLLSMAHLSAECLIQLTQVGYDV 243
Query: 77 GDFNQVVLQNVTKAQIKIRTKKDNVAGV 104
FN ++ QN K ++++R K +VA V
Sbjct: 244 TPFNNILKQN-AKKELRLRLAKKSVADV 270
>gnl|CDD|222768 PHA00002, A, DNA replication initiation protein gpA.
Length = 515
Score = 29.9 bits (67), Expect = 1.3
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 19 MKSRLKGAQKGHSLLKKKADALQMR-FRMILSKIIETKTL-MGEVMKEAAFSLAEAKFTT 76
++ G +K ++ LK K L + FR+ +S+ K L M + E L + +
Sbjct: 358 QAAKGLGNKKWNNSLKTKMALLPKKEFRIRMSRNFGMKLLSMAHLSAEVLIELTQVGYDV 417
Query: 77 GDFNQVVLQNVTKAQIKIRTKKDNVAGV 104
FNQ++ QN K ++++R K +VA V
Sbjct: 418 TPFNQILKQN-AKKELRLRLGKLSVADV 444
>gnl|CDD|182853 PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional.
Length = 520
Score = 29.6 bits (67), Expect = 1.5
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 47 ILSKIIETKTLMGEVMKEAA 66
IL + ET T++G V +AA
Sbjct: 207 ILPPVKETGTVLGHVTAKAA 226
>gnl|CDD|179382 PRK02195, PRK02195, V-type ATP synthase subunit D; Provisional.
Length = 201
Score = 29.1 bits (66), Expect = 1.8
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 11/91 (12%)
Query: 93 KIRTKKDNVAGVTLPVFESYQDGTDTYELAG----LARGGQQLAKLKKNYQTAIKLLVEL 148
K+ +N+AGV +P+ +S + Y L + G + LK+ Q I+ V
Sbjct: 83 KVEKDYENIAGVEVPILDSIEFEIIEYSLLNTPIWVDTG---IELLKELVQLKIEAEVLQ 139
Query: 149 ASLQTSFVTLDDVIKITNRRVNAIEHVIIPR 179
L L++ ++ T +RVN E V+IP
Sbjct: 140 ERLL----LLEEELRKTTQRVNLFEKVLIPE 166
>gnl|CDD|217279 pfam02903, Alpha-amylase_N, Alpha amylase, N-terminal ig-like
domain.
Length = 119
Score = 26.9 bits (60), Expect = 5.2
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 10/45 (22%)
Query: 92 IKIRTKKDNVAGVTLPVFESYQDGTDTYELAGLARGGQQLAKLKK 136
I++RTKKD+V V L ++ D YE + +KK
Sbjct: 25 IRLRTKKDDVERVYL-IYG------DPYEWGKWQ---SETVPMKK 59
>gnl|CDD|223994 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational
modification, protein turnover, chaperones].
Length = 647
Score = 27.7 bits (62), Expect = 7.1
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 187 IISELDELEREE-FYRLKKIQDKKKVIKAASEAFR 220
II E+ L + + LK + DK++ I +SE
Sbjct: 230 IIDEIGLLAQPLQWKLLKALLDKEQPIWGSSEPSS 264
>gnl|CDD|199887 cd02857, E_set_CDase_PDE_N, N-terminal Early set domain associated
with the catalytic domain of cyclomaltodextrinase and
pullulan-degrading enzymes. E or "early" set domains
are associated with the catalytic domain of the
cyclomaltodextrinase (CDase) and pullulan-degrading
enzymes at the N-terminal end. Members of this subgroup
include CDase, maltogenic amylase, and neopullulanase,
all of which are capable of hydrolyzing all or two of
the following three types of substrates:
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. The N-terminal
domain of the CDase and pullulan-degrading enzymes may
be related to the immunoglobulin and/or fibronectin type
III superfamilies. These domains are associated with
different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions.
Members of this family include members of the alpha
amylase family, sialidase, galactose oxidase, cellulase,
cellulose, hyaluronate lyase, chitobiase, and chitinase,
among others.
Length = 109
Score = 26.5 bits (59), Expect = 7.3
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 92 IKIRTKKDNVAGVTL 106
I++RT KD+V V L
Sbjct: 21 IRLRTAKDDVDSVFL 35
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 27.3 bits (61), Expect = 7.4
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 188 ISELDELEREEFYRLKKIQDKKKVIKAASEAFRKSRKYDEEQ------AFNMLEEEDQDI 241
+SE++EL+ + K+I K K E +K K +E+ A LE E QD
Sbjct: 43 LSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKALEAELQDK 102
Query: 242 LF 243
L
Sbjct: 103 LL 104
>gnl|CDD|234935 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed.
Length = 358
Score = 27.4 bits (61), Expect = 7.6
Identities = 29/102 (28%), Positives = 38/102 (37%), Gaps = 29/102 (28%)
Query: 102 AGVTLPVFESYQDGTDTYELAG---LARGGQQLAKLKKNYQTAIKLLVELASLQTSFVTL 158
A VTLPV E YQ Y A L+ Q +L+ L+ F L
Sbjct: 65 ADVTLPVLERYQRYLYGYRKANGEPLSTRTQ---------------RTQLSPLRVWFRWL 109
Query: 159 DDVIKITNRRV---NAIEHVIIPRIEKTL-AYIISELDELER 196
R N E + +P+ EK L I+SE E E+
Sbjct: 110 ------LKRHHILYNPAEDLELPKEEKRLPRQILSE-AETEQ 144
>gnl|CDD|236624 PRK09782, PRK09782, bacteriophage N4 receptor, outer membrane
subunit; Provisional.
Length = 987
Score = 27.6 bits (61), Expect = 7.9
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 175 VIIPRIEKTL-AYIISELDELEREEFYRLKKIQDKKKVIKAASEAFRKSRKYDEEQAFNM 233
VI PR++K L A ++ RE Y +++ D + +EA+R D + +
Sbjct: 43 VIYPRLDKALKAQKNNDEATAIREFEYIHQQVPDNIPLTLYLAEAYRHFGHDDRARL--L 100
Query: 234 LEE 236
LE+
Sbjct: 101 LED 103
>gnl|CDD|201520 pfam00945, Rhabdo_ncap, Rhabdovirus nucleocapsid protein. The
Nucleocapsid (N) Protein is said to have a "tight"
structure. The carboxyl end of the N-terminal domain
possesses an RNA binding domain. Sequence alignments
show 2 regions of reasonable conservation, approx.
64-103 and 201-329. A whole functional protein is
required for encapsidation to take place.
Length = 406
Score = 27.3 bits (61), Expect = 8.0
Identities = 13/80 (16%), Positives = 24/80 (30%), Gaps = 4/80 (5%)
Query: 62 MKEAAFSLAEAKFTTGDFNQVVLQNVTKAQIK--IRTKKDNVAGVTLPVFESYQDGTDTY 119
+ AA L+ A + Q ++ K + E+ + D
Sbjct: 319 LTVAALLLSYAFGSKATLEQRFFRDEKKYTEYRDDDGDNTDAPLADDGDDEAPK-SRDVV 377
Query: 120 E-LAGLARGGQQLAKLKKNY 138
E LA +L K++
Sbjct: 378 EWLAWYEDIMMKLTPDMKSF 397
>gnl|CDD|109900 pfam00862, Sucrose_synth, Sucrose synthase. Sucrose synthases
catalyze the synthesis of sucrose from UDP-glucose and
fructose. This family includes the bulk of the sucrose
synthase protein. However the carboxyl terminal region
of the sucrose synthases belongs to the glycosyl
transferase family pfam00534.
Length = 550
Score = 27.2 bits (60), Expect = 8.7
Identities = 28/128 (21%), Positives = 59/128 (46%), Gaps = 9/128 (7%)
Query: 84 LQNVTKAQIKIRTKKDNVAGVTLPVFESYQDGTDTYELAGLARG-GQQLAKLKKNYQTAI 142
+QN++ Q +R +D ++ TLP Y + ++ G RG G ++ + +
Sbjct: 194 IQNISALQSALRKAEDYLS--TLPPDTPYSEFEHKFQEIGFERGWGDTAERVLEMMHLLL 251
Query: 143 KLL--VELASLQTSFVTLD---DVIKITNRRVNAIEHVI-IPRIEKTLAYIISELDELER 196
LL + ++L+T + +V+ ++ A +V+ P + YI+ ++ LE
Sbjct: 252 DLLEAPDPSTLETFLGRIPMVFNVVILSPHGYFAQANVLGYPDTGGQVVYILDQVRALES 311
Query: 197 EEFYRLKK 204
E R+K+
Sbjct: 312 EMLVRIKQ 319
>gnl|CDD|237256 PRK12901, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1112
Score = 27.3 bits (61), Expect = 9.0
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 182 KTLAYIISELDELEREEFYRLKKIQDKKKVIKAASEAFRKSRKYDEEQAFNMLEE--EDQ 239
+TLA + S + E EEF +LKK + K+ AA E +++ + E AF ++++ E+Q
Sbjct: 856 RTLA-MESPITE---EEFNKLKKDELTDKLYDAALENYQRKMERIAEIAFPVIKQVYEEQ 911
Query: 240 DILF 243
++
Sbjct: 912 GNMY 915
>gnl|CDD|198353 cd07775, FGGY_AI-2K, Autoinducer-2 kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial autoinducer-2 (AI-2) kinases and
similar proteins. AI-2 is a small chemical
quorum-sensing signal involved in interspecies
communication in bacteria. Cytoplasmic autoinducer-2
kinase, encoded by the lsrK gene from Salmonella
enterica serovar Typhimurium lsr (luxS regulated)
operon, is the prototypical member of this subfamily.
AI-2 kinase catalyzes the phosphorylation of
intracellular AI-2 to phospho-AI-2, which leads to the
inactivation of lsrR, the repressor of the lsr operon.
Members of this family are homologs of glycerol
kinase-like proteins and belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 452
Score = 27.0 bits (60), Expect = 9.1
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 47 ILSKIIETKTLMGEVMKEAA 66
I ++ET T++G V EAA
Sbjct: 204 IFPPVVETGTVIGTVTNEAA 223
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
0.317 0.132 0.346
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,296,901
Number of extensions: 1197246
Number of successful extensions: 1523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1512
Number of HSP's successfully gapped: 84
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.2 bits)