RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2242
(246 letters)
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 120 bits (303), Expect = 4e-32
Identities = 57/162 (35%), Positives = 80/162 (49%), Gaps = 12/162 (7%)
Query: 3 IGDFNTYGGSFLYHLNEPSPLVAVGFVVGLDYTNPYLSPF-KEFQRFKTHPAVRPVFEGG 61
D G +++ L + VG V LD P LSPF + +RFK HPA+R + GG
Sbjct: 191 PLDVGPGGYGWIFPLGDG--HANVGIGVLLDD--PSLSPFLELLERFKEHPAIRKLLLGG 246
Query: 62 KRIAYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYE 121
K + Y A + EGG + P L G LVG AGF+N +G A+KSG LAAEA E
Sbjct: 247 KILEYAAGGIPEGGPASRP-LVGDGVLLVGDAAGFVNPLTGEGIRYAIKSGKLAAEAIAE 305
Query: 122 ALAEAGDEVSTGLEPKSYEDKIKSSWIYKELKEVRNCRPSFH 163
AL + ++ YE ++ S ++LK +R +
Sbjct: 306 ALEGGEEALAE------YERLLRKSLAREDLKSLRLLKLLLR 341
>gnl|CDD|182194 PRK10015, PRK10015, oxidoreductase; Provisional.
Length = 429
Score = 69.2 bits (169), Expect = 1e-13
Identities = 51/150 (34%), Positives = 80/150 (53%), Gaps = 9/150 (6%)
Query: 10 GGSFLYHLNEPSPLVAVGFVVGL-DYTNPYLSPFKEFQRFKTHPAVRPVFEGGKRIAYGA 68
GG FLY N+ S +++G V GL D + S + + FK HPA+RP+ GGK + Y A
Sbjct: 222 GGGFLY-TNKDS--ISLGLVCGLGDIAHAQKSVPQMLEDFKQHPAIRPLISGGKLLEYSA 278
Query: 69 RALNEGGLQAIPRLTFPGGCLVGCTAGF-LNVP-KIKGTHNAMKSGMLAAEATYEALAEA 126
+ EGGL +P+L G +VG AGF LN+ ++G A+ S AA A A
Sbjct: 279 HMVPEGGLAMVPQLVNDGVMIVGDAAGFCLNLGFTVRGMDLAIASAQAAATTVIAAKERA 338
Query: 127 GDEVSTGLEPKSYEDKIKSSWIYKELKEVR 156
D ++ L Y+ +++ S + ++++ R
Sbjct: 339 -DFSASSL--AQYKRELEQSCVMRDMQHFR 365
>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
Length = 428
Score = 55.7 bits (134), Expect = 5e-09
Identities = 39/120 (32%), Positives = 60/120 (50%), Gaps = 6/120 (5%)
Query: 10 GGSFLYHLNEPSPLVAVGFVVGLDYTNPYLSPFKE-FQRFKTHPAVRPVFEGGKRIAYGA 68
GG FLY NE + +++G V GL + + + + FK HPAV P+ GGK + Y A
Sbjct: 222 GGGFLY-TNENT--LSLGLVCGLHHLHDAKKSVPQMLEDFKQHPAVAPLIAGGKLVEYSA 278
Query: 69 RALNEGGLQAIPRLTFPGGCLVGCTAGF-LNVP-KIKGTHNAMKSGMLAAEATYEALAEA 126
+ E G+ +P L G + G AG +N+ I+G A+ +G AA+ A+
Sbjct: 279 HVVPEAGINMLPELVGDGVLIAGDAAGMCMNLGFTIRGMDLAIAAGEAAAKTVLSAMKSD 338
>gnl|CDD|218485 pfam05187, ETF_QO, Electron transfer flavoprotein-ubiquinone
oxidoreductase. Electron-transfer
flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the
inner mitochondrial membrane accepts electrons from
electron-transfer flavoprotein which is located in the
mitochondrial matrix and reduces ubiquinone in the
mitochondrial membrane. The two redox centres in the
protein, FAD and a [4Fe4S] cluster, are present in a
64-kDa monomer.
Length = 110
Score = 36.0 bits (84), Expect = 0.003
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 167 GLWGGLAYSGASIM-MKGIEPWTFK 190
GLW GLAY+G ++G PWT K
Sbjct: 1 GLWLGLAYAGLDQWILRGKSPWTLK 25
>gnl|CDD|225289 COG2440, FixX, Ferredoxin-like protein [Energy production and
conversion].
Length = 99
Score = 31.2 bits (71), Expect = 0.11
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 197 YVPLEDGSGERLQINAQNCIHCKTCDIKDP-TQNINWVVPEGGGGPAY 243
Y ++DG +L+ + + C+ C TC + P + I W P GG G Y
Sbjct: 52 YKLIDDG---KLRFDYEGCLECGTCRVLCPHSGLIQWRYPRGGFGITY 96
>gnl|CDD|233689 TIGR02023, BchP-ChlP, geranylgeranyl reductase. This model
represents a group of geranylgeranyl reductases specific
for the biosyntheses of bacteriochlorophyll and
chlorophyll. It is unclear whether the processes of
isoprenoid ligation to the chlorin ring and reduction of
the geranylgeranyl chain to a phytyl chain are
necessarily ordered the same way in all species (see
introduction to ) [Biosynthesis of cofactors, prosthetic
groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 388
Score = 32.8 bits (75), Expect = 0.13
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 71 LNEGG---LQAIPRLTFPGGCLVGCTAGFLNVPKIKGTHNAMKSGMLAAEATYEALAEAG 127
E ++ PR F LVG AG + +G + AMKSG +AA+A E L + G
Sbjct: 247 RREAAPIPMKPRPRWDFGRAMLVGDAAGLVTPASGEGIYFAMKSGQMAAQAIAEYL-QNG 305
Query: 128 DE 129
D
Sbjct: 306 DA 307
>gnl|CDD|235764 PRK06273, PRK06273, ferredoxin; Provisional.
Length = 165
Score = 30.4 bits (69), Expect = 0.43
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 9/44 (20%)
Query: 178 SIMMKGIEPWTFKWNSVYEYVPLEDGSGERLQINAQNCIHCKTC 221
+I M +EP V +P +I+ + C++C C
Sbjct: 65 AIEMIPVEPVKITEGYVKTKIP---------KIDYEKCVYCLYC 99
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 31.3 bits (71), Expect = 0.47
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 204 SGERLQINAQNCIHCKTCDIKDP 226
+ +Q+N Q CI CK+C + P
Sbjct: 76 VDDSIQVNQQKCIGCKSCVVACP 98
>gnl|CDD|183694 PRK12706, flgI, flagellar basal body P-ring protein; Provisional.
Length = 328
Score = 29.8 bits (67), Expect = 1.4
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 109 MKSGMLAAEATYEALAEAGDEVSTGLEPK-SYEDKIKSSWIYKELKEVRNCRPSFHSKLG 167
MK ++ A+ ++ S + + S+ ++I S K + E+ +F + +G
Sbjct: 2 MKKLIMLIILNLSLFAQE-NQASKNFKNENSFNNQISESVKLKNIAEICPTNSNFLTGIG 60
Query: 168 LWGGLAYSGASIMMKGI 184
+ GLA G S+ K I
Sbjct: 61 IVAGLADKGDSLKQKDI 77
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 29.4 bits (66), Expect = 2.4
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 43 KEFQRFKTHPAVRPVFEGGKRIAYGARALNEGGLQAIPRLTFP 85
+ F+ HP + V+E GK I A + EG L IP+L F
Sbjct: 980 RSFETTVDHPVM--VYENGKFIKKRAMDVKEGDLMLIPKLDFE 1020
>gnl|CDD|203605 pfam07262, DUF1436, Protein of unknown function (DUF1436). This
family consists of several hypothetical bacterial
proteins of around 160 residues in length. The function
of this family is unknown.
Length = 158
Score = 28.1 bits (63), Expect = 2.4
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 15/59 (25%)
Query: 128 DEVSTGLEPKSYEDKIKSSWIYKELKE------------VRNC---RPSFHSKLGLWGG 171
D K++ K+ + YK + + N RP+ H KL W
Sbjct: 69 DLEKLSEFYKNWVKKLMEKYGYKTKRALFKNMKFCGISLINNIITIRPTHHDKLEGWSA 127
>gnl|CDD|148936 pfam07592, DDE_Tnp_ISAZ013, Rhodopirellula transposase DDE domain.
These transposases are found in the planctomycete
Rhodopirellula baltica, the cyanobacterium Nostoc, and
the Gram-positive bacterium Streptomyces.
Length = 311
Score = 28.9 bits (65), Expect = 2.7
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 126 AGDEVSTGLEPKSYEDKIKSSWIYKELKEVRNCRPSFHSK 165
G V L+ K Y +K + +E+KE+ R FH +
Sbjct: 266 KGLNVVATLDEKEYPTGVKVT--DEEMKEINIERHKFHPE 303
>gnl|CDD|198234 cd10371, SH2_Src_Blk, Src homology 2 (SH2) domain found in B
lymphoid kinase (Blk). Blk is a member of the Src
non-receptor type tyrosine kinase family of proteins.
Blk is expressed in the B-cells. Unlike most other Src
members Blk lacks cysteine residues in the SH4 domain
that undergo palmitylation. Blk is required for the
development of IL-17-producing gamma-delta T cells.
Furthermore, Blk is expressed in lymphoid precursors
and, in this capacity, plays a role in regulating
thymus cellularity during ontogeny. Blk has a unique
N-terminal domain, an SH3 domain, an SH2 domain, a
kinase domain and a regulatory tail, as do the other
members of the family. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 100
Score = 27.3 bits (60), Expect = 3.0
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 66 YGARALNEGGLQAIPRLTFP 85
Y R+L+ GG PR+TFP
Sbjct: 58 YKIRSLDNGGYYISPRITFP 77
>gnl|CDD|205077 pfam12797, Fer4_2, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 22
Score = 25.5 bits (56), Expect = 3.0
Identities = 5/12 (41%), Positives = 6/12 (50%)
Query: 210 INAQNCIHCKTC 221
I+ CI C C
Sbjct: 5 IDEDKCIGCGAC 16
>gnl|CDD|177713 PLN00093, PLN00093, geranylgeranyl diphosphate reductase;
Provisional.
Length = 450
Score = 28.6 bits (64), Expect = 3.3
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 4/82 (4%)
Query: 43 KEFQRFKTHPAVRPVFEGGKRIAYGARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKI 102
K++QR T + GGK I A + E PR LVG AG++
Sbjct: 271 KKYQR-ATRNRAKDKIAGGKIIRVEAHPIPE---HPRPRRVRGRVALVGDAAGYVTKCSG 326
Query: 103 KGTHNAMKSGMLAAEATYEALA 124
+G + A KSG + AEA E
Sbjct: 327 EGIYFAAKSGRMCAEAIVEGSE 348
>gnl|CDD|188532 TIGR04017, WcaA, colanic acid biosynthesis glycosyl transferase
WcaA. This gene is one of the glycosyl transferases
involved in the biosynthesis of colanic acid, an
exopolysaccharide expressed in Enterobacteraceae
species.
Length = 279
Score = 27.7 bits (61), Expect = 5.0
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 97 LNVPKIKGTHNAMKSGMLAAEATYEALAEAGDEVSTGLE 135
LN P+++ THN + SG A +A+ +A E TG++
Sbjct: 57 LNDPRVRYTHNDINSGACAVRN--QAIMQAKGEYITGID 93
>gnl|CDD|219893 pfam08543, Phos_pyr_kin, Phosphomethylpyrimidine kinase. This
enzyme EC:2.7.4.7 is part of the Thiamine pyrophosphate
(TPP) synthesis pathway, TPP is an essential cofactor
for many enzymes.
Length = 246
Score = 27.8 bits (63), Expect = 5.3
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 107 NAMKSGMLAAEATYEALAE 125
+A+K+GML + EA+AE
Sbjct: 62 DAVKTGMLGSAEIIEAVAE 80
>gnl|CDD|193515 cd03895, M20_ArgE_DapE_like2, M20 Peptidases with similarity to
acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze
analogous reactions and share a common activator, the
metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad
range of substrates, including N-acetylornithine,
alpha-N-acetylmethionine and alpha-N-formylmethionine,
while DapE catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly bacterial, and have been inferred
by homology as being related to both ArgE and DapE.
Length = 399
Score = 27.5 bits (62), Expect = 6.1
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 109 MKSGMLAAEATYEALAEAG 127
MK G+ AA EAL AG
Sbjct: 115 MKGGLAAALFAVEALRAAG 133
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 27.5 bits (61), Expect = 8.0
Identities = 31/107 (28%), Positives = 48/107 (44%), Gaps = 14/107 (13%)
Query: 47 RFKTHPAVRPVF---EGGKRIAYG-ARALNEGGLQAIPRLTFPGGCLVGCTAGFLNVPKI 102
RF P ++ + E G R Y AL +G +++ P V T L ++
Sbjct: 216 RFNNIPQIKMIVVLGELGGRDEYSLVEALKQG------KVSKPVVAWVSGTCARLFKSEV 269
Query: 103 KGTHNAMKSG--MLAAEATYEALAEAGDEVSTGLEPKSYEDKIKSSW 147
+ H KSG M +A+A +AL +AG V T E + E IK ++
Sbjct: 270 QFGHAGAKSGGDMESAQAKNKALKDAGAIVPTSFE--ALEAAIKETF 314
>gnl|CDD|182197 PRK10018, PRK10018, putative glycosyl transferase; Provisional.
Length = 279
Score = 27.3 bits (60), Expect = 8.1
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 97 LNVPKIKGTHNAMKSGMLAAEATYEALAEAGDEVSTGLE 135
LN P+I HN + SG A +A+ A E TG++
Sbjct: 57 LNDPRITYIHNDINSGACAVRN--QAIMLAQGEYITGID 93
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 0.138 0.440
Gapped
Lambda K H
0.267 0.0665 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,978,417
Number of extensions: 1219058
Number of successful extensions: 1196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1191
Number of HSP's successfully gapped: 25
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
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 (26.3 bits)