RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4802
(103 letters)
>gnl|CDD|184098 PRK13507, PRK13507, formate--tetrahydrofolate ligase; Provisional.
Length = 587
Score = 91.3 bits (227), Expect = 5e-23
Identities = 34/58 (58%), Positives = 42/58 (72%)
Query: 35 EKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTEVSTSTEHQGC 92
EKF+N+KCR SG PD V+V T+RALKMHGGGP VV G+PL EYT+ + +GC
Sbjct: 330 EKFWNLKCRLSGLKPDCAVIVATIRALKMHGGGPKVVPGKPLPEEYTKENVGLVEKGC 387
>gnl|CDD|238266 cd00477, FTHFS, Formyltetrahydrofolate synthetase (FTHFS) catalyzes
the ATP-dependent activation of formate ion via its
addition to the N10 position of tetrahydrofolate. FTHFS
is a highly expressed key enzyme in both the
Wood-Ljungdahl pathway of autotrophic CO2 fixation
(acetogenesis) and the glycine synthase/reductase
pathways of purinolysis. The key physiological role of
this enzyme in acetogens is to catalyze the formylation
of tetrahydrofolate, an initial step in the reduction of
carbon dioxide and other one-carbon precursors to
acetate. In purinolytic organisms, the enzymatic
reaction is reversed, liberating formate from
10-formyltetrahydrofolate with concurrent production of
ATP.
Length = 524
Score = 87.6 bits (218), Expect = 8e-22
Identities = 31/41 (75%), Positives = 31/41 (75%)
Query: 34 MEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQ 74
EKFFNIKCR SG PDAVVLV TVRALKMHGG P V G
Sbjct: 291 AEKFFNIKCRYSGLKPDAVVLVATVRALKMHGGVPKVTLGL 331
>gnl|CDD|216402 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 557
Score = 85.6 bits (213), Expect = 5e-21
Identities = 27/35 (77%), Positives = 28/35 (80%)
Query: 34 MEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGP 68
EKFF+IKCR SG PDAVVLV TVRALKMHGG
Sbjct: 307 AEKFFDIKCRKSGLKPDAVVLVATVRALKMHGGVA 341
>gnl|CDD|178359 PLN02759, PLN02759, Formate--tetrahydrofolate ligase.
Length = 637
Score = 83.7 bits (207), Expect = 2e-20
Identities = 34/59 (57%), Positives = 39/59 (66%)
Query: 34 MEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTEVSTSTEHQGC 92
EKF NIKCR SG P V+V TVRALKMHGGGP+VV+G+PL YT + GC
Sbjct: 378 TEKFMNIKCRYSGLKPQCAVIVATVRALKMHGGGPAVVAGKPLDHAYTTENVELVEAGC 436
>gnl|CDD|240394 PTZ00386, PTZ00386, formyl tetrahydrofolate synthetase;
Provisional.
Length = 625
Score = 77.9 bits (192), Expect = 3e-18
Identities = 30/41 (73%), Positives = 32/41 (78%)
Query: 34 MEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQ 74
EKFFNIKCRTSG PDA VLV TVRALK HGG VV+G+
Sbjct: 373 CEKFFNIKCRTSGLKPDAAVLVATVRALKFHGGVEPVVAGK 413
>gnl|CDD|225354 COG2759, MIS1, Formyltetrahydrofolate synthetase [Nucleotide
transport and metabolism].
Length = 554
Score = 76.9 bits (190), Expect = 5e-18
Identities = 29/37 (78%), Positives = 31/37 (83%)
Query: 32 LWMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGP 68
L EKFF+IKCR+SG PDAVVLV TVRALKMHGG P
Sbjct: 303 LGAEKFFDIKCRSSGLKPDAVVLVATVRALKMHGGVP 339
>gnl|CDD|237403 PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional.
Length = 557
Score = 75.2 bits (186), Expect = 3e-17
Identities = 24/34 (70%), Positives = 27/34 (79%)
Query: 35 EKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGP 68
EKF +IKCR +G PDAVV+V TVRALKMHGG
Sbjct: 309 EKFLDIKCRKAGLKPDAVVIVATVRALKMHGGVA 342
>gnl|CDD|237404 PRK13506, PRK13506, formate--tetrahydrofolate ligase; Provisional.
Length = 578
Score = 65.0 bits (159), Expect = 7e-14
Identities = 24/43 (55%), Positives = 27/43 (62%)
Query: 34 MEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPL 76
EKF NIK R SGK PD VLV T+RALK + G + GQ L
Sbjct: 321 FEKFCNIKARQSGKAPDCAVLVATLRALKANSGLYDLRPGQAL 363
>gnl|CDD|107321 cd06326, PBP1_STKc_like, Type I periplasmic binding domain of
uncharacterized extracellular ligand-binding proteins.
The type I periplasmic binding domain of uncharacterized
extracellular ligand-binding proteins, some of which
contain a conserved catalytic serine/threonine protein
kinase (STKc) domain in the N-terminal region. Members
of this group are sequence-similar to the branched-chain
amino acid ABC transporter
leucine-isoleucine-valine-binding protein (LIVBP); their
ligand specificity has not been determined
experimentally, however.
Length = 336
Score = 30.2 bits (69), Expect = 0.14
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 12/43 (27%)
Query: 49 PDAVVLVTT-------VRALKMHGGGP-----SVVSGQPLKPE 79
P AV++V +RAL+ GGG S V L
Sbjct: 192 PQAVIMVGAYKAAAAFIRALRKAGGGAQFYNLSFVGADALARL 234
>gnl|CDD|225785 COG3246, COG3246, Uncharacterized conserved protein [Function
unknown].
Length = 298
Score = 26.6 bits (59), Expect = 2.3
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 49 PDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTEVSTSTE 88
DAV+ +TT + S L+PE ++ S
Sbjct: 76 GDAVINLTTGEGGDLVMPTEERASPWALRPEALSMNLSEF 115
>gnl|CDD|199828 cd09941, SH2_Grb2_like, Src homology 2 domain found in Growth
factor receptor-bound protein 2 (Grb2) and similar
proteins. The adaptor proteins here include homologs
Grb2 in humans, Sex muscle abnormal protein 5 (Sem-5)
in Caenorhabditis elegans, and Downstream of receptor
kinase (drk) in Drosophila melanogaster. They are
composed of one SH2 and two SH3 domains. Grb2/Sem-5/drk
regulates the Ras pathway by linking the tyrosine
kinases to the Ras guanine nucleotide releasing protein
Sos, which converts Ras to the active GTP-bound state.
The SH2 domain of Grb2/Sem-5/drk binds class II
phosphotyrosyl peptides while its SH3 domain binds to
Sos and Sos-derived, proline-rich peptides. Besides it
function in Ras signaling, Grb2 is also thought to play
a role in apoptosis. Unlike most SH2 structures in
which the peptide binds in an extended conformation
(such that the +3 peptide residue occupies a
hydrophobic pocket in the protein, conferring a modest
degree of selectivity), Grb2 forms several hydrogen
bonds via main chain atoms with the side chain of +2
Asn. 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 = 95
Score = 25.7 bits (57), Expect = 2.7
Identities = 6/12 (50%), Positives = 10/12 (83%)
Query: 29 KYWLWMEKFFNI 40
KY+LW+ KF ++
Sbjct: 62 KYFLWVVKFNSL 73
>gnl|CDD|240205 cd05700, S1_Rrp5_repeat_hs9, S1_Rrp5_repeat_hs9: Rrp5 is a
trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9).
Rrp5 is found in eukaryotes but not in prokaryotes or
archaea.
Length = 65
Score = 25.2 bits (55), Expect = 3.6
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 5/34 (14%)
Query: 44 TSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLK 77
+ G++ VL + + H G +V G LK
Sbjct: 20 SGGQVSGLTVLAS-----RYHKEGVNVTPGCKLK 48
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 25.4 bits (56), Expect = 3.8
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 40 IKCRTSGKIPDAVVLVTTVRALKMHGG 66
+ C + D V++VTT AL + G
Sbjct: 50 LLCLLALLAADLVIIVTTPEALAVLGA 76
>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 25.7 bits (57), Expect = 4.1
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 34 MEKFF----NIKCRTSGKIPDAVVLVTTVRA 60
+EK F +I +G DA VLV RA
Sbjct: 61 VEKIFKIDDHIGMAIAGLAADAQVLVRYARA 91
>gnl|CDD|185600 PTZ00410, PTZ00410, NAD-dependent SIR2; Provisional.
Length = 349
Score = 25.6 bits (56), Expect = 5.3
Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 9 RESAEIVYALLILEGHLWPSKYW 31
RE E+ Y++ E LWP +
Sbjct: 78 REKPEVFYSIA-REMDLWPGHFQ 99
>gnl|CDD|223820 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase
domains [DNA replication, recombination, and repair].
Length = 593
Score = 25.7 bits (57), Expect = 5.8
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 2 IPQAKPCRESAEIVYALLILEGHLWP 27
+ K +AE A L LE L P
Sbjct: 153 VKLEKATEYAAEDADATLRLESILEP 178
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
0.320 0.136 0.437
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,062,261
Number of extensions: 402208
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 21
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
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 (24.0 bits)