RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6711
(135 letters)
>gnl|CDD|233003 TIGR00512, salvage_mtnA, S-methyl-5-thioribose-1-phosphate
isomerase. The delineation of this family was based in
part on a discussion and neighbor-joining phylogenetic
study, by Kyrpides and Woese, of archaeal and other
proteins homologous to the alpha, beta, and delta
subunits of eukaryotic initiation factor 2B (eIF-2B), a
five-subunit molecule that catalyzes GTP recycling for
eIF-2. This clade is now recognized to include the
methionine salvage pathway enzyme MtnA [Amino acid
biosynthesis, Aspartate family].
Length = 331
Score = 89.6 bits (223), Expect = 2e-22
Identities = 29/54 (53%), Positives = 40/54 (74%)
Query: 11 QIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
Q+AV AKHH VPF++AAP ++IDL+ +G I IEERP +E+THV G+ +A
Sbjct: 250 QLAVLAKHHGVPFYVAAPTSTIDLETKDGAEIPIEERPPEEVTHVGGVRIAPPG 303
>gnl|CDD|235578 PRK05720, mtnA, methylthioribose-1-phosphate isomerase; Reviewed.
Length = 344
Score = 78.3 bits (194), Expect = 3e-18
Identities = 25/55 (45%), Positives = 39/55 (70%)
Query: 10 LQIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
Q+A++AK+H VPF++AAP ++IDL + +G I IEER +E+T V G+ +A
Sbjct: 249 YQLAIAAKYHGVPFYVAAPSSTIDLTLADGKEIPIEERDPEEVTEVGGVRIAPEG 303
>gnl|CDD|223260 COG0182, COG0182, Predicted translation initiation factor 2B
subunit, eIF-2B alpha/beta/delta family [Translation,
ribosomal structure and biogenesis].
Length = 346
Score = 70.4 bits (173), Expect = 2e-15
Identities = 24/55 (43%), Positives = 38/55 (69%)
Query: 10 LQIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
Q+AV AKHH +PF++AAP ++ID ++ +G+ I IEER +E+ V G+ +A
Sbjct: 252 YQLAVLAKHHGIPFYVAAPLSTIDFELKSGEDIPIEERDPEEVLEVGGVRIAPEG 306
>gnl|CDD|216240 pfam01008, IF-2B, Initiation factor 2 subunit family. This family
includes initiation factor 2B alpha, beta and delta
subunits from eukaryotes, initiation factor 2B subunits
1 and 2 from archaebacteria and some proteins of unknown
function from prokaryotes. Initiation factor 2 binds to
Met-tRNA, GTP and the small ribosomal subunit. Members
of this family have also been characterized as
5-methylthioribose- 1-phosphate isomerases, an enzyme of
the methionine salvage pathway. The crystal structure of
Ypr118w, a non-essential, low-copy number gene product
from Saccharomyces cerevisiae, reveals a dimeric protein
with two domains and a putative active site cleft.
Length = 281
Score = 59.6 bits (145), Expect = 1e-11
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 10 LQIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASDCG 66
Q+A+ AK H VPF++ A D P + I IEER +E+ + G+ +A +
Sbjct: 199 YQLALLAKAHNVPFYVVAETYKFDPRFPLDEDIFIEERDPEEVLYRTGVRIAPENLK 255
>gnl|CDD|233008 TIGR00524, eIF-2B_rel, eIF-2B alpha/beta/delta-related
uncharacterized proteins. This model, eIF-2B_rel,
describes half of a superfamily, where the other half
consists of eukaryotic translation initiation factor 2B
(eIF-2B) subunits alpha, beta, and delta. It is unclear
whether the eIF-2B_rel set is monophyletic, or whether
they are all more closely related to each other than to
any eIF-2B subunit because the eIF-2B clade is highly
derived. Members of this branch of the family are all
uncharacterized with respect to function and are found
in the Archaea, Bacteria, and Eukarya, although a number
are described as putative translation intiation factor
components. Proteins found by eIF-2B_rel include at
least three clades, including a set of uncharacterized
eukaryotic proteins, a set found in some but not all
Archaea, and a set universal so far among the Archaea
and closely related to several uncharacterized bacterial
proteins [Unknown function, General].
Length = 303
Score = 57.5 bits (139), Expect = 8e-11
Identities = 23/55 (41%), Positives = 34/55 (61%)
Query: 10 LQIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
Q+AV AK ++PFF+AAP ++ D G+ IVIEER +E+ V G+ +A
Sbjct: 221 YQLAVLAKEFRIPFFVAAPLSTFDTKTSCGEDIVIEERDPEEVAQVGGVRIAPLG 275
>gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit
beta; Validated.
Length = 356
Score = 52.7 bits (126), Expect = 5e-09
Identities = 21/50 (42%), Positives = 31/50 (62%)
Query: 12 IAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVA 61
+AV AK H +PFF AP ++ID+ + +G I IEER +E+ G +A
Sbjct: 264 LAVLAKEHGIPFFTVAPLSTIDMSLKSGKEIPIEERSPEEVLTCGGCRIA 313
>gnl|CDD|180547 PRK06371, PRK06371, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 329
Score = 50.3 bits (120), Expect = 3e-08
Identities = 20/56 (35%), Positives = 33/56 (58%)
Query: 13 AVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASDCGSK 68
AV AK + +PF++AAP ++ D I +GD I IEER E+ + G + + ++
Sbjct: 242 AVLAKVNGIPFYVAAPGSTFDFSIKSGDEIPIEERDENEVLEINGCRIGPQESHAR 297
>gnl|CDD|180362 PRK06036, PRK06036, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 339
Score = 43.6 bits (103), Expect = 7e-06
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 13 AVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
+V AK H++PF++AAP ++ D + G + IEER E+ + +A D
Sbjct: 252 SVLAKEHEIPFYVAAPLSTFDFEGWEGS-VKIEERDPDELRYCGKTQIAPKD 302
>gnl|CDD|236282 PRK08535, PRK08535, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 310
Score = 37.2 bits (87), Expect = 0.001
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 12/47 (25%)
Query: 11 QIAVSAKHHKVPFFIAA------PWTSIDLDIPNGDAIVIEERPSQE 51
QIA++A +VPF +AA P T + G+ + IEER E
Sbjct: 213 QIALAAHEARVPFMVAAETYKFSPKTLL------GELVEIEERDPTE 253
>gnl|CDD|168237 PRK05772, PRK05772, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 363
Score = 36.3 bits (84), Expect = 0.003
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 13 AVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
AV A +PF+ AP ++ DL + + + IEER E+ + G+ + D
Sbjct: 273 AVIAHELGIPFYALAPTSTFDL-KSDVNDVKIEERDPNEVRTIRGVPITPED 323
>gnl|CDD|188057 TIGR00511, ribulose_e2b2, ribose-1,5-bisphosphate isomerase, e2b2
family. The delineation of this family was based
originally, in part, on a discussion and
neighbor-joining phylogenetic study by Kyrpides and
Woese of archaeal and other proteins homologous to the
alpha, beta, and delta subunits of eukaryotic initiation
factor 2B (eIF-2B), a five-subunit molecule that
catalyzes GTP recycling for eIF-2. Recently, Sato, et
al. assigned the function ribulose-1,5 bisphosphate
isomerase [Energy metabolism, Other].
Length = 301
Score = 34.7 bits (80), Expect = 0.007
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 11 QIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQE 51
Q+A++A+ +VPF +AA G+ + IEER E
Sbjct: 208 QLALAAREARVPFMVAAETYKFHPKTITGELVEIEERDPTE 248
>gnl|CDD|218284 pfam04832, SOUL, SOUL heme-binding protein. This family represents
a group of putative heme-binding proteins. Our family
includes archaeal and bacterial homologues.
Length = 174
Score = 33.8 bits (78), Expect = 0.012
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 20 KVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEM 52
V F + + + + L P + I E P++ +
Sbjct: 85 TVSFVMPSGYQAETLPAPLDPDVRIREVPARTV 117
>gnl|CDD|224105 COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B
alpha/beta/delta family [Translation, ribosomal
structure and biogenesis].
Length = 301
Score = 29.6 bits (67), Expect = 0.37
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 10 LQIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQE 51
+A++A+ +VPF++ A + IE R E
Sbjct: 211 SPLALAARELRVPFYVVAESYKFVPKTLLDTLVEIELRDPLE 252
>gnl|CDD|219350 pfam07253, Gypsy, Gypsy protein. This family consists of several
Gypsy/Env proteins from Drosophila and Ceratitis fruit
fly species. Gypsy is an endogenous retrovirus of
Drosophila melanogaster. Phylogenetic studies suggest
that occasional horizontal transfer events of gypsy
occur between Drosophila species. Gypsy possesses
infective properties associated with the products of the
envelope gene that might be at the origin of these
interspecies transfers. This family contains many
members with full-length matches; however, it also
includes a number of very short sequences and short
matches of sequences with other unrelated domains on
them, which cannot be excluded. These matches may
represent remnants of once-functional genes.
Length = 472
Score = 27.1 bits (60), Expect = 2.8
Identities = 10/40 (25%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 82 EDLPEMSIVELEDVKIIQDDHTIHKMSARINIIFSDCDKF 121
E+ P + ++E +K++Q ++ IH + + F C+K
Sbjct: 204 ENTPIVELLEAAKIKVLQSENIIHIIIKYPKVTFE-CNKV 242
>gnl|CDD|129252 TIGR00148, TIGR00148, UbiD family decarboxylase. The member of
this family in E. coli is UbiD,
3-octaprenyl-4-hydroxybenzoate carboxy-lyase. The family
described by This model, however, is broad enough that
it is likely to contain several different
decarboxylases. Found in bacteria, archaea, and yeast,
with two members in A. fulgidus. No homologs were
detected besides those classified as orthologs. The
member from H. pylori has a C-terminal extension of just
over 100 residues that is shared in part by the Aquifex
aeolicus homolog [Unknown function, General].
Length = 438
Score = 27.0 bits (60), Expect = 3.3
Identities = 22/99 (22%), Positives = 36/99 (36%), Gaps = 32/99 (32%)
Query: 31 SIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASDCGSKGTFQSHSGSINKVEDLPEMSIV 90
+ DL++P IV+E + T + +G F H+G + V P
Sbjct: 241 TNDLEVPADAEIVLEGTITAGETEL------------EGPFGDHTGYYDIVRPEP----- 283
Query: 91 ELEDVKIIQDDHTIHKMSARINIIFSDCDKFMTNYGKPP 129
+I T+ +M R + I+ T G PP
Sbjct: 284 ------VI----TVKRMYHREDPIY-----HATYPGGPP 307
>gnl|CDD|214566 smart00216, VWD, von Willebrand factor (vWF) type D domain. Von
Willebrand factor contains several type D domains: D1
and D2 are present within the N-terminal propeptide
whereas the remaining D domains are required for
multimerisation.
Length = 163
Score = 25.8 bits (57), Expect = 7.2
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 59 HVAASDCGSKGTFQSHSGSINKVEDLPEMSIVELE----DVKIIQDDHTI 104
+V A DC S+ TF ++ + V++E ++++ D+ +
Sbjct: 36 YVLAQDCSSEPTFSVLLKNVPCGGGATCLKSVKVELNGDEIELKDDNGKV 85
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 0.136 0.413
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,923,246
Number of extensions: 602581
Number of successful extensions: 454
Number of sequences better than 10.0: 1
Number of HSP's gapped: 450
Number of HSP's successfully gapped: 26
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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: 53 (24.3 bits)