RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13593
(264 letters)
>gnl|CDD|214540 smart00164, TBC, Domain in Tre-2, BUB2p, and Cdc16p. Probable
Rab-GAPs. Widespread domain present in Gyp6 and Gyp7,
thereby giving rise to the notion that it performs a
GTP-activator activity on Rab-like GTPases.
Length = 216
Score = 209 bits (534), Expect = 4e-68
Identities = 102/222 (45%), Positives = 131/222 (59%), Gaps = 13/222 (5%)
Query: 12 QGVPRSKRGEVWLFLAQQYCKQNPMDTSKFPNYNVSYEQLLKQ----LTSHQHAILLDLG 67
+GVP S RG VW L PMDTS + Y +LLK+ S H I DL
Sbjct: 3 KGVPPSLRGVVWKLLLNAQ----PMDTSADKDL---YSRLLKETAPDDKSIVHQIEKDLR 55
Query: 68 RTFPSHPYYSSPLGPGQLSLFNVLKAYSLLDPEVGYCQGLSFVAGVLLLH-HSEEQAFMM 126
RTFP H ++ GPGQ SL VLKAY+L +PEVGYCQG++F+A LLL EE AF
Sbjct: 56 RTFPEHSFFQDKEGPGQESLRRVLKAYALYNPEVGYCQGMNFLAAPLLLVMEDEEDAFWC 115
Query: 127 LRHLMFRRGLRQTYLPDMAALQVQLYQFSRLLLDHYPDLHAHFDTHEVHPTLYAAPWLLT 186
L LM R G YLPDM+ LQ+ L Q RL+ ++ PDL+ H + P+LYA W LT
Sbjct: 116 LVKLMERYGPN-FYLPDMSGLQLDLLQLDRLVKEYDPDLYKHLKDLGITPSLYALRWFLT 174
Query: 187 LFSSQFPLGFVTRVFDMVLVENPEIVFRVMLSLLGQHRENLL 228
LF+ + PL V R++D++ E + +FRV L+LL HR+ LL
Sbjct: 175 LFARELPLEIVLRIWDVLFAEGSDFLFRVALALLKLHRDVLL 216
>gnl|CDD|215997 pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain. Identification of a
TBC domain in GYP6_YEAST and GYP7_YEAST, which are
GTPase activator proteins of yeast Ypt6 and Ypt7,
implies that these domains are GTPase activator proteins
of Rab-like small GTPases.
Length = 206
Score = 180 bits (459), Expect = 6e-57
Identities = 78/213 (36%), Positives = 116/213 (54%), Gaps = 9/213 (4%)
Query: 17 SKRGEVWLFLAQQYCKQNPMDTSKFPNYNVSYEQLLKQLTSHQHAILLDLGRTFPSHPYY 76
S RGEVW L + + + + + L + + + I D+ RTFP H ++
Sbjct: 2 SLRGEVWKLLLGNLSESK-----QRDSVSQYSKLLKLEDSPDEEQIEKDVPRTFPHHFFF 56
Query: 77 SSPLGPGQLSLFNVLKAYSLLDPEVGYCQGLSFVAGVLLLHH-SEEQAFMMLRHLMFRRG 135
+ G GQ L +LKAYS+ +P+VGYCQG++F+A LLL EE+AF L+
Sbjct: 57 KN--GEGQQQLRRILKAYSIYNPDVGYCQGMNFIAAPLLLVVLDEEEAFWCFVSLLEY-L 113
Query: 136 LRQTYLPDMAALQVQLYQFSRLLLDHYPDLHAHFDTHEVHPTLYAAPWLLTLFSSQFPLG 195
LR +LP LQ LY F LL H P+L+ H + P+L+A+ W LTLF+ + PL
Sbjct: 114 LRDFFLPSFPGLQRDLYVFEELLKKHDPELYKHLQKLGLDPSLFASKWFLTLFARELPLE 173
Query: 196 FVTRVFDMVLVENPEIVFRVMLSLLGQHRENLL 228
V R++D+ L +FRV L++L + R+ LL
Sbjct: 174 TVLRLWDLFLEGGKFFLFRVALAILKRFRKELL 206
>gnl|CDD|227535 COG5210, COG5210, GTPase-activating protein [General function
prediction only].
Length = 496
Score = 159 bits (404), Expect = 1e-45
Identities = 77/234 (32%), Positives = 120/234 (51%), Gaps = 8/234 (3%)
Query: 12 QGVPRSKRGEVWLFLAQQYCKQNPMDTSKFPNY--NVSYEQLLKQLTSHQ-HAILLDLGR 68
+G+P RG+VW FL Y ++ + K T I DL R
Sbjct: 211 KGIPNELRGDVWEFLLGIG----FDLDKNPGLYERLLNLHREAKIPTQEIISQIEKDLSR 266
Query: 69 TFPSHPYYSSPLGPGQLSLFNVLKAYSLLDPEVGYCQGLSFVAGVLLLH-HSEEQAFMML 127
TFP + + + + +L VLKAYSL +PEVGY QG++F+A LLL SEEQAF L
Sbjct: 267 TFPDNSLFQTEISIRAENLRRVLKAYSLYNPEVGYVQGMNFLAAPLLLVLESEEQAFWCL 326
Query: 128 RHLMFRRGLRQTYLPDMAALQVQLYQFSRLLLDHYPDLHAHFDTHEVHPTLYAAPWLLTL 187
L+ GL +L +++ L L L+ + P+L+ H V ++A W LTL
Sbjct: 327 VKLLKNYGLPGYFLKNLSGLHRDLKVLDDLVEELDPELYEHLLREGVVLLMFAFRWFLTL 386
Query: 188 FSSQFPLGFVTRVFDMVLVENPEIVFRVMLSLLGQHRENLLRCENFETIMDYLK 241
F +FPL + R++D + +E ++F++ L++L R+ LL+ ++ E + LK
Sbjct: 387 FVREFPLEYALRIWDCLFLEGSSMLFQLALAILKLLRDKLLKLDSDELLDLLLK 440
>gnl|CDD|182642 PRK10678, moaE, molybdopterin guanine dinucleotide biosynthesis
protein MoaE; Provisional.
Length = 150
Score = 31.6 bits (72), Expect = 0.18
Identities = 30/93 (32%), Positives = 41/93 (44%), Gaps = 25/93 (26%)
Query: 155 SRLLLDHYPDLHAHFDTHEVHPTLYAAPWLLTLFSSQFPLGFVT---RVFDMVLVENP-- 209
L L+HYP + T A ++ S++PLG VT RV ++ P
Sbjct: 48 KALTLEHYPGM-----------TEKALAEIVDEARSRWPLGRVTVIHRVGEL----WPGD 92
Query: 210 EIVFRVMLSLLGQHRENLLRCENFETIMDYLKT 242
EIVF + + HR + F IMDYLKT
Sbjct: 93 EIVF---VGVTSAHRSSAFEAGQF--IMDYLKT 120
>gnl|CDD|179628 PRK03669, PRK03669, mannosyl-3-phosphoglycerate phosphatase;
Reviewed.
Length = 271
Score = 29.6 bits (67), Expect = 1.3
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 14/54 (25%)
Query: 144 MAALQVQLYQFSRL---LLDHYPDLHAHFDTHEVHPTLYAAPWLLTLFSSQFPL 194
M +LQ L F+ L LLD + T++ P AAPWL L +Q P+
Sbjct: 1 MLSLQDPLLIFTDLDGTLLDSH--------TYDWQP---AAPWLTRLREAQVPV 43
>gnl|CDD|202118 pfam02126, PTE, Phosphotriesterase family.
Length = 308
Score = 29.4 bits (66), Expect = 1.6
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 156 RLLLDHYPDLHAHFDTH--EVHPTLYAAPWLLTLFSSQFPL-GFVTRVFDMVLVENPEIV 212
R+LL H D+ F + H Y+ LLT + G V D +LVENP+
Sbjct: 251 RILLSH--DITTKFRSMKYGGHG--YSHILLLTNVIPKLRQRGVTQEVLDKILVENPKQF 306
Query: 213 F 213
Sbjct: 307 L 307
>gnl|CDD|178585 PLN03008, PLN03008, Phospholipase D delta.
Length = 868
Score = 29.7 bits (66), Expect = 2.1
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 133 RRGLRQTYLPDMAALQVQLYQFSRLL 158
RRG+R+TY P QV+LYQ + ++
Sbjct: 195 RRGVRRTYFPVRKGSQVRLYQDAHVM 220
>gnl|CDD|226690 COG4239, COG4239, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 341
Score = 29.3 bits (66), Expect = 2.1
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 12/61 (19%)
Query: 176 PTLYAAPWLLTLFSSQFPLGFVTRVFDMVLVENPEIVFRVMLSLLGQHRENLLRCENFET 235
PTLY LL + +S F F + M+L F M SL+G R LR N +
Sbjct: 187 PTLY----LLIILASIFQPNFWWLLGIMLL-------FGWM-SLVGVVRAEFLRARNLDY 234
Query: 236 I 236
+
Sbjct: 235 V 235
>gnl|CDD|223818 COG0747, DdpA, ABC-type dipeptide transport system, periplasmic
component [Amino acid transport and metabolism].
Length = 556
Score = 29.1 bits (65), Expect = 2.5
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 71 PSHPYYSSPLGPGQLSLFNVLKAYSLLDPEVGY 103
P P Y+ + ++ KA +LLD E GY
Sbjct: 347 PLVPGYNPDIEKYAADAYDPEKAKALLD-EAGY 378
>gnl|CDD|181206 PRK08042, PRK08042, formate hydrogenlyase subunit 3; Reviewed.
Length = 593
Score = 29.0 bits (65), Expect = 2.9
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 180 AAPWLLTLFSSQFPLGFVTR-------VFDMVLVENPEIVFRVML 217
AAPWLL + S+ PL + ++L+ P + F +M
Sbjct: 460 AAPWLLPMLSAAVPLPLEPANTTVSQPMITLLLIACPLLPFIIMA 504
>gnl|CDD|226092 COG3562, KpsS, Capsule polysaccharide export protein [Cell envelope
biogenesis, outer membrane].
Length = 403
Score = 28.3 bits (63), Expect = 4.8
Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 4/55 (7%)
Query: 133 RRGLRQTYLPDMAALQVQLYQFSRLLLDHYPDLHAHFDTHEVHPTLYAAPWLLTL 187
+LP MA+ + + L +PD H TLY A W +
Sbjct: 155 PEDNIGGFLP-MASFAILYNLGAFFLSRKFPDYIHH---RTPTATLYLAFWNRSG 205
>gnl|CDD|176516 cd08574, GDPD_GDE_2_3_6, Glycerophosphodiester phosphodiesterase
domain of mammalian glycerophosphodiester
phosphodiesterase GDE2, GDE3, GDE6-like proteins. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in mammalian
glycerophosphodiester phosphodiesterase
domain-containing protein subtype 5 (GDE2), subtype 2
(GDE3), subtype 1 (GDE6), and their eukaryotic homologs.
Mammalian GDE2, GDE3, and GDE6 show very high sequence
similarity to each other and have been classified into
the same family. Although they are all transmembrane
proteins, based on different pattern of tissue
distribution, these enzymes might display diverse
cellular functions. Mammalian GDE2 is primarily
expressed in mature neurons. It selectively hydrolyzes
glycerophosphocholine (GPC) and mainly functions in a
complex with an antioxidant scavenger peroxiredoxin1
(Prdx1) to control motor neuron differentiation in the
spinal cord. Mammalian GDE3 is specifically expressed
in bone tissues and spleen. It selectively hydrolyzes
extracellular glycerophosphoinositol (GPI) to generate
inositol 1-phosphate (Ins1P) and glycerol and functions
as an inducer of osteoblast differentiation. Mammalian
GDE6 is predominantly expressed in the spermatocytes of
testis, and its specific physiological function has not
been elucidated yet.
Length = 252
Score = 27.7 bits (62), Expect = 5.9
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 47 SYEQLLKQLTSHQHAILLDLGRTFPSHPYYSS 78
S +LL+ H +++ DL R P+HPYY S
Sbjct: 115 SLAELLRLAKKHNKSVIFDLRRPPPNHPYYQS 146
>gnl|CDD|144140 pfam00434, VP7, Glycoprotein VP7.
Length = 326
Score = 27.8 bits (62), Expect = 6.1
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 233 FETIMDYLKTNITVMDKRT 251
F T++DY+ I VM KR+
Sbjct: 296 FYTVVDYINQIIQVMSKRS 314
>gnl|CDD|198080 smart01012, ANTAR, ANTAR (AmiR and NasR transcription
antitermination regulators) is an RNA-binding domain
found in bacterial transcription antitermination
regulatory proteins. The majority of the domain
consists of a coiled-coil.
Length = 55
Score = 25.5 bits (57), Expect = 6.2
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 112 GVLLLHH--SEEQAFMMLRHLMFRRGLRQTYLPDMAA 146
G+L+ SEE+AF +LR L R ++ L D+A
Sbjct: 19 GILMERRGLSEEEAFELLRKLAMDRNVK---LRDVAE 52
>gnl|CDD|163683 cd07945, DRE_TIM_CMS, Leptospira interrogans citramalate synthase
(CMS) and related proteins, N-terminal catalytic TIM
barrel domain. Citramalate synthase (CMS) catalyzes the
conversion of pyruvate and acetyl-CoA to (R)-citramalate
in the first dedicated step of the citramalate pathway.
Citramalate is only found in Leptospira interrogans and
a few other microorganisms. This family belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 280
Score = 27.7 bits (62), Expect = 6.3
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 118 HSEEQAFMMLRHLMFRRGLRQTYLPD----MAALQVQLYQFSRLLLDHYPDLHAHFDTH 172
S + F ++ L +++ LPD ++ + Y + ++ YP+LH F H
Sbjct: 144 DSPDYVFQLVDFLS-DLPIKRIMLPDTLGILSPFET--YTYISDMVKRYPNLHFDFHAH 199
>gnl|CDD|188633 cd00502, DHQase_I, Type I 3-dehydroquinase, (3-dehydroquinate
dehydratase or DHQase). Type I 3-dehydroquinase,
(3-dehydroquinate dehydratase or DHQase). Catalyzes the
cis-dehydration of 3-dehydroquinate via a covalent imine
intermediate to produce dehydroshikimate. Dehydroquinase
is the third enzyme in the shikimate pathway, which is
involved in the biosynthesis of aromatic amino acids.
Type I DHQase exists as a homodimer. Type II
3-dehydroquinase also catalyzes the same overall
reaction, but is unrelated in terms of sequence and
structure, and utilizes a completely different reaction
mechanism.
Length = 225
Score = 27.3 bits (61), Expect = 6.5
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 72 SHPYYSSPLGPGQLSLFNVLKAYSL 96
++ P PGQLS+ + +A SL
Sbjct: 201 TYASLPEPSAPGQLSVEELKQALSL 225
>gnl|CDD|182645 PRK10682, PRK10682, putrescine transporter subunit:
periplasmic-binding component of ABC superfamily;
Provisional.
Length = 370
Score = 27.5 bits (61), Expect = 7.4
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 25 FLAQQYCKQ--NPMDTSKFPNYNVSYEQLLKQLTSH 58
FL +Q P+D SK PN+ +LLK + H
Sbjct: 88 FLERQLTAGVFQPLDKSKLPNWKNLDPELLKLVAKH 123
>gnl|CDD|227479 COG5150, COG5150, Class 2 transcription repressor NC2, beta subunit
(Dr1) [Transcription].
Length = 148
Score = 26.9 bits (59), Expect = 9.0
Identities = 14/50 (28%), Positives = 20/50 (40%)
Query: 28 QQYCKQNPMDTSKFPNYNVSYEQLLKQLTSHQHAILLDLGRTFPSHPYYS 77
+ Y KQ SKF + +S E+LL+Q L +F P
Sbjct: 95 KSYQKQKESKISKFKDSGLSMEELLRQQEELFQNARLRFEHSFEDDPVKG 144
>gnl|CDD|217833 pfam03997, VPS28, VPS28 protein.
Length = 187
Score = 26.7 bits (59), Expect = 9.9
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 226 NLLRC-----ENFETIMDYLKTNITVMD 248
N+ +C +NF T+MD L+ NI D
Sbjct: 92 NIAKCIAEIVQNFITVMDALRLNINAKD 119
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
0.326 0.139 0.427
Gapped
Lambda K H
0.267 0.0848 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,728,941
Number of extensions: 1321664
Number of successful extensions: 1614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1603
Number of HSP's successfully gapped: 27
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (25.9 bits)