RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1297
(427 letters)
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 99.6 bits (249), Expect = 1e-25
Identities = 28/94 (29%), Positives = 45/94 (47%)
Query: 143 GQLELWQYFLSGSLGGIVTAALVAPGERIKCLLQVQEGGLSNVYSGPVDVIRKLIQQHGL 202
L L+G + G + A + P + +K LQ G S Y G +D +K+ ++ G+
Sbjct: 1 SPLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGI 60
Query: 203 GSVFKGFSATLLRDVPAFGAYYAMYETVKHVFSG 236
++KG LLR PA Y+ YET+K +
Sbjct: 61 RGLYKGLLPNLLRVAPAAAIYFGTYETLKKLLLK 94
Score = 66.9 bits (164), Expect = 6e-14
Identities = 28/71 (39%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 22 AMPADVLKTRLQ--TAPEDKYPHGIRSVLSEMLEREGPRTLYRGATPVLLRAIPANAACF 79
P DV+KTRLQ A + GI ++ + EG R LY+G P LLR PA A F
Sbjct: 23 TYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGIRGLYKGLLPNLLRVAPAAAIYF 82
Query: 80 LGIEWTLQLLR 90
E +LL
Sbjct: 83 GTYETLKKLLL 93
Score = 41.9 bits (99), Expect = 4e-05
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 250 KTTPLVGTITAGSMAGISYWIVAMPADVLKTRLQ--TAPEDKYPHGIRSVLSEML 302
+ ++ AG +AG V P DV+KTRLQ A + GI ++
Sbjct: 1 SPLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIY 55
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 57.1 bits (138), Expect = 5e-09
Identities = 41/143 (28%), Positives = 70/143 (48%), Gaps = 19/143 (13%)
Query: 151 FLSGSLGGIVTAALVAPGERIKCLLQVQE------GGLSNVYSGPVDVIRKLIQQHGLGS 204
FL G + ++ VAP ER+K L+Q Q+ G YSG V+ R++ ++ G+ S
Sbjct: 11 FLMGGISAAISKTAVAPIERVKMLIQTQDSIPEIKSGKVPRYSGIVNCFRRVSKEQGVLS 70
Query: 205 VFKGFSATLLRDVP--AFGAYYAMYETVKHVFSGQGDSVIEVSDQTRKTTPLVGT-ITAG 261
+++G +A ++R P AF +A + K++F +Q G I +G
Sbjct: 71 LWRGNTANVIRYFPTQAFN--FAFKDYFKNMFPKY--------NQKTDFWKFFGVNILSG 120
Query: 262 SMAGISYWIVAMPADVLKTRLQT 284
+AG S ++ P D +TRL +
Sbjct: 121 GLAGASSLLIVYPLDFARTRLAS 143
Score = 51.7 bits (124), Expect = 3e-07
Identities = 35/154 (22%), Positives = 75/154 (48%), Gaps = 13/154 (8%)
Query: 91 MLDCVTKILQKEKIFGFYKGMGAPLVGVAPLNALNYFGYGTGLK--FFTNEKNMGQLELW 148
+++C ++ +++ + ++G A ++ P A N F + K F + + W
Sbjct: 55 IVNCFRRVSKEQGVLSLWRGNTANVIRYFPTQAFN-FAFKDYFKNMFPKYNQKT---DFW 110
Query: 149 QYF----LSGSLGGIVTAALVAPGE--RIKCLLQVQEGGLSNVYSGPVDVIRKLIQQHGL 202
++F LSG L G + +V P + R + + +GG ++G D + K+ +Q G
Sbjct: 111 KFFGVNILSGGLAGASSLLIVYPLDFARTRLASDIGKGG-DREFTGLFDCLMKISKQTGF 169
Query: 203 GSVFKGFSATLLRDVPAFGAYYAMYETVKHVFSG 236
S+++GF ++ + GAY+ +Y++ K + G
Sbjct: 170 LSLYQGFGVSVQGIIVYRGAYFGLYDSAKALLFG 203
Score = 49.8 bits (119), Expect = 1e-06
Identities = 34/131 (25%), Positives = 63/131 (48%), Gaps = 11/131 (8%)
Query: 91 MLDCVTKILQKEKIFGFYKGMGAPLVGVAPLNALNYFGYGTGLK--FFTNEKNMGQLELW 148
+ DC+ KI ++ Y+G G + G+ YFG K F N+KN L W
Sbjct: 156 LFDCLMKISKQTGFLSLYQGFGVSVQGIIVYRG-AYFGLYDSAKALLFGNDKNTNILYKW 214
Query: 149 QYFLSGSLGGIVTAALVA-PGERIK---CLLQVQEGGLSNVYSGPVDVIRKLIQQHGLGS 204
++ ++ + A L++ P + ++ ++ ++ Y+G +D +K+++ GLG
Sbjct: 215 --AVAQTV--TILAGLISYPFDTVRRRMMMMSGRKAKSEIQYTGTLDCWKKILKNEGLGG 270
Query: 205 VFKGFSATLLR 215
FKG A +LR
Sbjct: 271 FFKGAWANVLR 281
>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
Length = 259
Score = 44.9 bits (106), Expect = 3e-05
Identities = 52/201 (25%), Positives = 90/201 (44%), Gaps = 29/201 (14%)
Query: 92 LDCVTKILQKEKIFGF------YKGMGAPLVGVAPLNALNYFGYGTGLKFFT-NEKNMGQ 144
+D + +Q +K F F Y G+ LVG P +A Y Y K T +N+ +
Sbjct: 24 IDSIKTNIQAKKSFSFSDIKKLYSGILPTLVGTVPASAFFYCFYELSKKLLTEYRENISK 83
Query: 145 LELWQYFLSGSLGGIVTAALVAPGERIKCLLQVQEGGLSNVYSGPVDVIR---KLIQQHG 201
L Y +S S+ I + P E +K +QV SG + V++ ++ Q+ G
Sbjct: 84 TNL--YLISTSIAEITACIVRLPFEIVKQNMQV---------SGNISVLKTIYEITQREG 132
Query: 202 LGS-VFKGFSATLLRDVPAFGAYYAMYETVKHVFSGQGDSVIEVSDQTRKTTPLVGTITA 260
L S + K + ++R++P Y ++ET+K + D ++K + I
Sbjct: 133 LPSFLGKSYFVMIVREIPFDCIQYFLWETLKE--KAKKD----FGKFSKKYPSITSAICG 186
Query: 261 GSMAGISYWIVAMPADVLKTR 281
G GI+ ++ P DV+K+R
Sbjct: 187 GLAGGIAGFLTT-PVDVIKSR 206
Score = 39.9 bits (93), Expect = 0.001
Identities = 33/141 (23%), Positives = 66/141 (46%), Gaps = 26/141 (18%)
Query: 145 LELWQYFLSGSLGGIVTAALVAPGERIKCLLQVQEGGLSNVYSGPVDVIRKLIQQHGLGS 204
+E + ++G+L G++ A++ P + IK +Q ++ S I+KL
Sbjct: 1 MEHFHNLVTGALSGVIVDAVLYPIDSIKTNIQAKK-------SFSFSDIKKL-------- 45
Query: 205 VFKGFSATLLRDVPAFGAYYAMYETVKHVFSGQGDSVIEVSDQTRKTTPLVGTITAGSMA 264
+ G TL+ VPA +Y YE K + + +++ ++ L+ T S+A
Sbjct: 46 -YSGILPTLVGTVPASAFFYCFYELSKKLLTEYRENI------SKTNLYLIST----SIA 94
Query: 265 GISYWIVAMPADVLKTRLQTA 285
I+ IV +P +++K +Q +
Sbjct: 95 EITACIVRLPFEIVKQNMQVS 115
>gnl|CDD|221106 pfam11398, DUF2813, Protein of unknown function (DUF2813). This
entry contains YjbD from Escherichia coli, which is
annotated as a nucleotide triphosphate hydrolase.
Length = 373
Score = 32.6 bits (75), Expect = 0.41
Identities = 22/85 (25%), Positives = 31/85 (36%), Gaps = 14/85 (16%)
Query: 17 FPDFPAMPADVLK---TRLQTAPEDKYPHGIRSVLSEMLEREGPRTLYRGATPVLL---- 69
LK L+ + + +L+ +L+ +GP L R A P+LL
Sbjct: 234 SLLDTQRLWRKLKSLNQLLKQPNNKQLRLLLLGLLNTLLQAKGPVELRRIARPILLLEDP 293
Query: 70 --RAIPANAACFLGIEWTL-QLLRM 91
R P L I W L LL M
Sbjct: 294 EGRLHPTM----LAIAWELLNLLPM 314
>gnl|CDD|148461 pfam06857, ACP, Malonate decarboxylase delta subunit (MdcD).
This family consists of several bacterial malonate
decarboxylase delta subunit (MdcD) proteins. Malonate
decarboxylase of Klebsiella pneumoniae consists of four
different subunits and catalyzes the conversion of
malonate plus H+ to acetate and CO2. The catalysis
proceeds via acetyl and malonyl thioester residues with
the phosphribosyl-dephospho-CoA prosthetic group of the
acyl carrier protein (ACP) subunit. MdcC is the (apo)
ACP subunit. The family also contains the CitD family
of citrate lyase acyl carrier proteins.
Length = 87
Score = 30.2 bits (69), Expect = 0.47
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 21 PAMPADVLKTRLQTAPEDKYPHGIRSVLSEMLEREGPRTLY-----RGATPVLLRA 71
PA P L+ L+++ ++ IR+V+ + L R G + +GA ++RA
Sbjct: 22 PADPGG-LEIELESSVAKQFGAQIRAVIRDTLARLGVTNVKVSINDKGALDCVIRA 76
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-binding
motif. Extended SDRs are distinct from classical SDRs.
In addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 30.7 bits (70), Expect = 1.3
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 17 FPDFPA-MPADVLKTRLQTAPEDKYPHGIRSVLSEMLEREGPRTLYRGAT 65
+ D P +P + L+TR + APE P GI SE + +LY GA+
Sbjct: 129 YGDLPNYLPLEELETRYELAPEGWSPAGI----SESFPLDFSHSLY-GAS 173
>gnl|CDD|183144 PRK11460, PRK11460, putative hydrolase; Provisional.
Length = 232
Score = 29.6 bits (67), Expect = 2.7
Identities = 21/78 (26%), Positives = 29/78 (37%), Gaps = 22/78 (28%)
Query: 190 VDVIRKLIQQHGLG---SVFKGFSA-------------TLLRDVPAFGAYYA------MY 227
++ +R QQ G+G + GFS L V AF YA
Sbjct: 88 IETVRYWQQQSGVGASATALIGFSQGAIMALEAVKAEPGLAGRVIAFSGRYASLPETAPT 147
Query: 228 ETVKHVFSGQGDSVIEVS 245
T H+ G D VI+V+
Sbjct: 148 ATTIHLIHGGEDPVIDVA 165
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 28.9 bits (65), Expect = 4.7
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 184 NVYSGPVDVIRKL---IQQHGLGSVFKGFSATLLRDVPAFGAY-------YAMYETVKHV 233
NV+ G + + + ++ +G G++ S L++ PA G Y Y++ + ++
Sbjct: 106 NVF-GLLRLAQAFAPVLKANGGGAIVNLNSVASLKNFPAMGTYSASKSAAYSLTQGLRAE 164
Query: 234 FSGQGDSVIEV 244
+ QG V+ V
Sbjct: 165 LAAQGTLVLSV 175
>gnl|CDD|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 28.1 bits (63), Expect = 7.9
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 311 YCLSYVFTSLDLSYRCYIPECESPDGPFYA 340
LS SL LS R P E+PD F+A
Sbjct: 83 ELLSNYLPSLSLSSRRLAPN-EAPDTTFFA 111
>gnl|CDD|177429 PHA02604, rI.-1, hypothetical protein; Provisional.
Length = 126
Score = 27.1 bits (60), Expect = 9.6
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 374 SFQDDIVEKCTQWIYKYPEE--KNILVEDDIVEKCTQWIYK 412
+F D+++++ + IYK ++ L DDI C Q YK
Sbjct: 85 AFLDELLQEAEE-IYKELPSALQSTL--DDITGLCYQTKYK 122
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 0.138 0.426
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,357,735
Number of extensions: 2165118
Number of successful extensions: 1838
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1827
Number of HSP's successfully gapped: 20
Length of query: 427
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 327
Effective length of database: 6,502,202
Effective search space: 2126220054
Effective search space used: 2126220054
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: 60 (26.8 bits)