RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9801
(132 letters)
>gnl|CDD|216424 pfam01302, CAP_GLY, CAP-Gly domain. Cytoskeleton-associated
proteins (CAPs) are involved in the organisation of
microtubules and transportation of vesicles and
organelles along the cytoskeletal network. A conserved
motif, CAP-Gly, has been identified in a number of
CAPs, including CLIP-170 and dynactins. The crystal
structure of Caenorhabditis elegans F53F4.3 protein
CAP-Gly domain was recently solved. The domain contains
three beta-strands. The most conserved sequence, GKNDG,
is located in two consecutive sharp turns on the
surface, forming the entrance to a groove.
Length = 67
Score = 90.3 bits (225), Expect = 3e-25
Identities = 34/67 (50%), Positives = 44/67 (65%), Gaps = 1/67 (1%)
Query: 23 IGDRVYV-GGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLF 81
+GDRV V GG + G + ++G FAPG W GV LD+P GKNDG V RYF+C P++G+F
Sbjct: 1 VGDRVEVLGGGRRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVDGVRYFECPPKYGIF 60
Query: 82 APVHKVS 88
KV
Sbjct: 61 VRPSKVE 67
>gnl|CDD|214997 smart01052, CAP_GLY, Cytoskeleton-associated proteins (CAPs) are
involved in the organisation of microtubules and
transportation of vesicles and organelles along the
cytoskeletal network. A conserved motif, CAP-Gly, has
been identified in a number of CAPs, including CLIP-170
and dynactins. The crystal structure of Caenorhabditis
elegans F53F4.3 protein CAP-Gly domain was recently
solved. The domain contains three beta-strands. The
most conserved sequence, GKNDG, is located in two
consecutive sharp turns on the surface, forming the
entrance to a groove.
Length = 68
Score = 83.0 bits (206), Expect = 2e-22
Identities = 35/68 (51%), Positives = 45/68 (66%), Gaps = 2/68 (2%)
Query: 23 IGDRVYVGGT-KSGRIAFIGETKFAPGDWAGVVLDDPV-GKNDGQVGQARYFQCEPRFGL 80
+GDRV VGG + G + ++G T FAPG W GV LD+P+ GKNDG V RYF+C P+ G+
Sbjct: 1 VGDRVEVGGGGRRGTVRYVGPTPFAPGVWVGVELDEPLRGKNDGSVKGVRYFECPPKHGI 60
Query: 81 FAPVHKVS 88
F KV
Sbjct: 61 FVRPSKVE 68
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 79.0 bits (194), Expect = 3e-18
Identities = 32/59 (54%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 23 IGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPRFGLF 81
+ DRV +G G + FIG+TKF G W G+ LDDPVGKNDG V RYF C+ R G+F
Sbjct: 6 VNDRVLLGDKF-GTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRHGIF 63
>gnl|CDD|107309 cd06314, PBP1_tmGBP, Periplasmic sugar-binding domain of Thermotoga
maritima glucose-binding protein (tmGBP) and its close
homologs. Periplasmic sugar-binding domain of
Thermotoga maritima glucose-binding protein (tmGBP) and
its close homologs from other bacteria. They are a
member of the type I periplasmic binding protein
superfamily which consists of two domains connected by a
three-stranded hinge. TmGBP is specific for glucose and
its binding pocket is buried at the interface of the two
domains. TmGBP also exhibits high thermostability and
the highest structural similarity to E. coli glucose
binding protein (ecGBP).
Length = 271
Score = 28.1 bits (63), Expect = 1.3
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 11/50 (22%)
Query: 3 ALWKAYDSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAG 52
AL KA +++T D+D+ SGR +IG +A G AG
Sbjct: 72 ALNKAAAGIKLITTDSDA-----------PDSGRYVYIGTDNYAAGRTAG 110
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 27.7 bits (62), Expect = 1.9
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 3 ALWKAYDSSQVLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDP 58
AL K S VL D ++ + V+ G + A I + PGD +++ P
Sbjct: 49 ALAKFLGRSPVLKLDREAAV----VFGSGAGANIEALIFLLRLNPGD--AILVPAP 98
>gnl|CDD|215057 PLN00105, PLN00105, malate/L-lactate dehydrogenase; Provisional.
Length = 330
Score = 27.5 bits (61), Expect = 2.2
Identities = 16/62 (25%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 7 AYDSSQVLTEDTDSFIIGDRV-YVGGTKSGRIAFIGE---TKFAPGDWAGVVLDDPVGKN 62
A D +LT D + + G + GG K +A E W V KN
Sbjct: 190 AIDKQGILTTDPNEVLDGGAIDTFGGYKGSGLALTVELLAGALVGAAWGEDVTGKMSAKN 249
Query: 63 DG 64
G
Sbjct: 250 WG 251
>gnl|CDD|233489 TIGR01603, maj_tail_phi13, phage major tail protein, phi13
family. This model describes a set of proteins that
share low levels of sequence similarity but similar
lengths and similar patterns of charged, hydrophobic,
and Gly/Pro residues. All members (except one
attributed to mouse embryo cDNA) belong to phage of
Gram-positive bacteria. Several are identified as phage
major tail proteins. Some members of this family have
additional C-terminal regions of about 100 residues not
included in this model [Mobile and extrachromosomal
element functions, Prophage functions].
Length = 190
Score = 25.9 bits (57), Expect = 6.4
Identities = 10/37 (27%), Positives = 13/37 (35%)
Query: 13 VLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGD 49
VL F +GG K ++ GE A D
Sbjct: 13 VLDSTAGVFTYETPKKLGGLKEAKVEPKGELVTAYAD 49
>gnl|CDD|178778 PLN03240, PLN03240, putative Low-temperature-induced protein;
Provisional.
Length = 626
Score = 26.3 bits (57), Expect = 6.6
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 46 APGDWAGVVLD-----DPVGKNDGQVGQARYFQCEPRFGLFAPVHKVSKSPMSGTKRLSC 100
APG G+ D DP+GK+ G++G A R GL + K KS TK +
Sbjct: 204 APGSHGGLSNDQSKVTDPIGKSTGEIGAASTVSAIGRLGLGTDLQK--KSHGLDTKPAAP 261
Query: 101 AVHHGLRRSGSR 112
H G+ S+
Sbjct: 262 GSHGGMSNYQSK 273
>gnl|CDD|226734 COG4284, COG4284, UDP-glucose pyrophosphorylase [Carbohydrate
transport and metabolism].
Length = 472
Score = 26.2 bits (58), Expect = 6.7
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 3/52 (5%)
Query: 72 FQC--EPRFGLFAPVHKVSKSPMSGTKRLSCAV-HHGLRRSGSRESITSNFS 120
PRFG F+P+ + S + +C + L +I+ N
Sbjct: 389 GGLLLVPRFGEFSPLKNLEGSHFDNVETFTCGIPRIPLILELEGLTISGNVL 440
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 25.7 bits (57), Expect = 6.9
Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 11/80 (13%)
Query: 25 DRVYVGGTKSGRIAFIGETKFAPGDWAGV---VLDD---PVGKNDGQVGQARYFQCEPRF 78
D V + G IA + E A D +LD+ + + V A F
Sbjct: 57 DGPLVRAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDG-----F 111
Query: 79 GLFAPVHKVSKSPMSGTKRL 98
L A ++ + + + L
Sbjct: 112 RLIATMNPLDRGLNELSPAL 131
>gnl|CDD|225321 COG2524, COG2524, Predicted transcriptional regulator, contains
C-terminal CBS domains [Transcription].
Length = 294
Score = 25.8 bits (57), Expect = 7.2
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 17 DTDSFIIGDRVYVGGTKSGRIAFIGE 42
D IGD V VG T ++ G+
Sbjct: 123 DIRKINIGDSVRVGPTPVNKLVVEGK 148
>gnl|CDD|176215 cd08253, zeta_crystallin, Zeta-crystallin with NADP-dependent
quinone reductase activity (QOR). Zeta-crystallin is a
eye lens protein with NADP-dependent quinone reductase
activity (QOR). It has been cited as a structural
component in mammalian eyes, but also has homology to
quinone reductases in unrelated species. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
acts in the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent
single electron transfer. QOR is a member of the medium
chain dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. Alcohol dehydrogenase in
the liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site, and a structural
zinc in a lobe of the catalytic domain. NAD(H)-binding
occurs in the cleft between the catalytic and
coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose
of NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 25.6 bits (57), Expect = 9.2
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 16 EDTDSFIIGDRVYVGGTKSGRI 37
E D +GDRV++ GR
Sbjct: 74 EGVDGLKVGDRVWLTNLGWGRR 95
>gnl|CDD|100011 cd06154, YjgF_YER057c_UK114_like_6, This group of proteins belong
to a large family of YjgF/YER057c/UK114-like proteins
present in bacteria, archaea, and eukaryotes with no
definitive function. The conserved domain is similar
in structure to chorismate mutase but there is no
sequence similarity and no functional connection.
Members of this family have been implicated in
isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF)
biosynthesis, as well as threonine anaerobic
degradation (tdcF) and mitochondrial DNA maintenance
(Ibm1). This domain homotrimerizes forming a distinct
intersubunit cavity that may serve as a small molecule
binding site.
Length = 119
Score = 25.2 bits (56), Expect = 9.3
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 22 IIGDRVYVGGTKSGRIAFIGETKFAPGD 49
+G+ V+V GT + + PGD
Sbjct: 18 RVGNWVFVSGT----TGYDYDGMVMPGD 41
>gnl|CDD|132249 TIGR03205, pimA, dicarboxylate--CoA ligase PimA. PimA, a member of
a large family of acyl-CoA ligases, is found in a
characteristic operon pimFABCDE for the metabolism of
pimelate and related compounds. It is found, so far, in
Bradyrhizobium japonicum and several strains of
Rhodopseudomonas palustris. PimA from R. palustris was
shown to be active as a CoA ligase for C(7) to C(14)
dicarboxylates and fatty acids.
Length = 541
Score = 25.7 bits (56), Expect = 9.9
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 78 FG-LFAPVHKVSKSPMSGTKRLSCAVHHGLRRSGSRESITSNFSNVTTTSVK 128
FG L A V SP+ G + LS H L SG+R ITS+ + + ++K
Sbjct: 89 FGALKAGARVVHLSPLDGERALS----HKLSDSGARLLITSDLAALLPMALK 136
>gnl|CDD|238623 cd01298, ATZ_TRZ_like, TRZ/ATZ family contains enzymes from the
atrazine degradation pathway and related hydrolases.
Atrazine, a chlorinated herbizide, can be catabolized
by a variety of different bacteria. The first three
steps of the atrazine dehalogenation pathway are
catalyzed by atrazine chlorohydrolase (AtzA),
hydroxyatrazine ethylaminohydrolase (AtzB), and
N-isopropylammelide N-isopropylaminohydrolase (AtzC).
All three enzymes belong to the superfamily of metal
dependent hydrolases. AtzA and AtzB, beside other
related enzymes are represented in this CD.
Length = 411
Score = 25.6 bits (57), Expect = 9.9
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 13 VLTEDTDSFIIGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLD 56
++T D + V V + GRI +G P A V+D
Sbjct: 8 IVTTDPRRVLEDGDVLV---EDGRIVAVGPALPLPAYPADEVID 48
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
0.318 0.133 0.400
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,464,534
Number of extensions: 553302
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 413
Number of HSP's successfully gapped: 21
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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: 53 (24.1 bits)