RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10593
(275 letters)
>gnl|CDD|240218 cd05792, S1_eIF1AD_like, S1_eIF1AD_like: eukaryotic translation
initiation factor 1A domain containing protein
(eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is
also known as MGC11102 protein. Little is known about
the function of eIF1AD. S1-like RNA-binding domains are
found in a wide variety of RNA-associated proteins,
including translation initiation factor IF1A (also
referred to as eIF1A in eukaryotes). eIF1A is essential
for translation initiation. eIF1A acts synergistically
with eIF1 to mediate assembly of ribosomal initiation
complexes at the initiation codon and maintain the
accuracy of this process by recognizing and
destabilizing aberrant preinitiation complexes from the
mRNA. Without eIF1A and eIF1, 43S ribosomal
preinitiation complexes can bind to the cap-proximal
region, but are unable to reach the initiation codon.
eIF1a also enhances the formation of 5'-terminal
complexes in the presence of other translation
initiation factors.
Length = 78
Score = 109 bits (275), Expect = 8e-31
Identities = 41/74 (55%), Positives = 59/74 (79%)
Query: 27 NIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIE 86
IV++ + GNNLH++E +G +Y VSMP KFR NIWIK GDFV+V+PIEEG+KVKAEI
Sbjct: 2 QIVRVLGSKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIV 61
Query: 87 QILDKKYISFLKQQ 100
+IL + ++ ++K++
Sbjct: 62 KILTRDHVKYIKEE 75
Score = 42.0 bits (99), Expect = 1e-05
Identities = 13/28 (46%), Positives = 22/28 (78%)
Query: 137 EEGNKVKAEIEQILDKKYISFLKQQNSW 164
EEG+KVKAEI +IL + ++ ++K++ W
Sbjct: 51 EEGDKVKAEIVKILTRDHVKYIKEEGLW 78
>gnl|CDD|128900 smart00652, eIF1a, eukaryotic translation initiation factor 1A.
Length = 83
Score = 79.6 bits (197), Expect = 3e-19
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 21 VPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNK 80
ED I ++ + GN ++ G++ +PGK R +WI+ GD V+V P +
Sbjct: 1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQ-D 59
Query: 81 VKAEIEQILDKKYISFLKQQLKLP 104
VKA+I K + +LK++ +LP
Sbjct: 60 VKADIIYKYTKDEVRWLKKEGELP 83
>gnl|CDD|239903 cd04456, S1_IF1A_like, S1_IF1A_like: Translation initiation factor
IF1A-like, S1-like RNA-binding domain. IF1A is also
referred to as eIF1A in eukaryotes and aIF1A in archaea.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. IF1A is essential for
translation initiation. eIF1A acts synergistically with
eIF1 to mediate assembly of ribosomal initiation
complexes at the initiation codon and maintain the
accuracy of this process by recognizing and
destabilizing aberrant preinitiation complexes from the
mRNA. Without eIF1A and eIF1, 43S ribosomal
preinitiation complexes can bind to the cap-proximal
region, but are unable to reach the initiation codon.
eIF1a also enhances the formation of 5'-terminal
complexes in the presence of other translation
initiation factors. This protein family is only found in
eukaryotes and archaea.
Length = 78
Score = 75.7 bits (186), Expect = 8e-18
Identities = 36/73 (49%), Positives = 51/73 (69%)
Query: 28 IVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQ 87
IV++ + GNN H++E G++ VS+PGK R NIWIK GDF+IV PIEEG VKA+I
Sbjct: 3 IVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIF 62
Query: 88 ILDKKYISFLKQQ 100
+ K ++ LK++
Sbjct: 63 VYCKDHVRSLKKE 75
>gnl|CDD|216345 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1. This
family includes both the eukaryotic translation factor
eIF-1A and the bacterial translation initiation factor
IF-1.
Length = 65
Score = 69.5 bits (171), Expect = 1e-15
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 28 IVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQ 87
I ++T+ GN ++E G + +PGK R IWI GDFV+V+ +K K +I
Sbjct: 6 IGQVTEMLGNGRFEVELEDGHERLAHIPGKRRKRIWILRGDFVLVELSPY-DKTKGDIIY 64
Query: 88 I 88
Sbjct: 65 R 65
>gnl|CDD|129614 TIGR00523, eIF-1A, eukaryotic/archaeal initiation factor 1A.
Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A
for Archaea. Also called eIF-4C [Protein synthesis,
Translation factors].
Length = 99
Score = 42.2 bits (99), Expect = 2e-05
Identities = 24/74 (32%), Positives = 35/74 (47%)
Query: 31 ITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILD 90
I Q G ++ G+ +PGK + IWI+ GD VIVKP E K +I
Sbjct: 25 IEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEFQGDDKCDIVWRYT 84
Query: 91 KKYISFLKQQLKLP 104
K + +LK++ L
Sbjct: 85 KTQVEWLKRKGYLK 98
>gnl|CDD|240219 cd05793, S1_IF1A, S1_IF1A: Translation initiation factor IF1A,
also referred to as eIF1A in eukaryotes and aIF1A in
archaea, S1-like RNA-binding domain. S1-like
RNA-binding domains are found in a wide variety of
RNA-associated proteins. IF1A is essential for
translation initiation. eIF1A acts synergistically with
eIF1 to mediate assembly of ribosomal initiation
complexes at the initiation codon and maintain the
accuracy of this process by recognizing and
destabilizing aberrant preinitiation complexes from the
mRNA. Without eIF1A and eIF1, 43S ribosomal
preinitiation complexes can bind to the cap-proximal
region, but are unable to reach the initiation codon.
eIF1a also enhances the formation of 5'-terminal
complexes in the presence of other translation
initiation factors. This protein family is only found
in eukaryotes and archaea.
Length = 77
Score = 39.0 bits (92), Expect = 1e-04
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 47 GEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEI 85
G+K + GK R +WI GD V+V P + + KA+I
Sbjct: 22 GKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDD-KADI 59
>gnl|CDD|179708 PRK04012, PRK04012, translation initiation factor IF-1A;
Provisional.
Length = 100
Score = 37.2 bits (87), Expect = 0.001
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 55 PGKFRNNIWIKPGDFVIVKPI----EEGNKV----KAEIEQILDKKYISF 96
PGK + +WI+ GD VIV P E+ + + K +++ + K YIS
Sbjct: 51 PGKMKKRMWIREGDVVIVAPWDFQDEKADIIWRYTKPQVDWLRRKGYISE 100
>gnl|CDD|223438 COG0361, InfA, Translation initiation factor 1 (IF-1)
[Translation, ribosomal structure and biogenesis].
Length = 75
Score = 34.9 bits (81), Expect = 0.004
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 20 RVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFR-NNIWIKPGDFVIVKPIEEG 78
P+++ + + N ++E +G + + GK R N I I PGD V+V+
Sbjct: 2 AKPDEIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYD 61
Query: 79 NKVKAEIE 86
K I
Sbjct: 62 LT-KGRIV 68
>gnl|CDD|239912 cd04466, S1_YloQ_GTPase, S1_YloQ_GTPase: YloQ GTase family (also
known as YjeQ and CpgA), S1-like RNA-binding domain.
Proteins in the YloQ GTase family bind the ribosome and
have GTPase activity. The precise role of this family
is unknown. The protein structure is composed of three
domains: an N-terminal S1 domain, a central GTPase
domain, and a C-terminal zinc finger domain. This
N-terminal S1 domain binds ssRNA. The central GTPase
domain contains nucleotide-binding signature motifs: G1
(walker A), G3 (walker B) and G4 motifs. Experiments
show that the bacterial YloQ and YjeQ proteins have low
intrinsic GTPase activity. The C-terminal zinc-finger
domain has structural similarity to a portion of the
DNA-repair protein Rad51. This suggests a possible role
for this GTPase as a regulator of translation, perhaps
as a translation initiation factor. This family is
classified based on the N-terminal S1 domain.
Length = 68
Score = 32.1 bits (74), Expect = 0.038
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 28 IVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIE 86
I+K + +E G+ Y + GKFR GD V +P ++G V IE
Sbjct: 5 IIKAI----GGFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPEDDGEGV---IE 57
Query: 87 QILDKK 92
+IL +K
Sbjct: 58 EILPRK 63
>gnl|CDD|215699 pfam00079, Serpin, Serpin (serine protease inhibitor). Structure
is a multi-domain fold containing a bundle of helices
and a beta sandwich.
Length = 369
Score = 29.9 bits (68), Expect = 1.5
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 97 LKQQLKLPPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNK---EEGNKVKAEIEQILDKK 153
L L P +++ +I FQ + KP + TL + N+ ++G K+K + Q+L K
Sbjct: 49 LLSVLGFPELDDEEIHEGFQSLLSSLNKPDKGYTLKIANRLFVDKGLKLKPDFLQLLKKY 108
Query: 154 Y------ISF------LKQQNSW 164
Y + F KQ NSW
Sbjct: 109 YGAEVESVDFSDPAEARKQINSW 131
>gnl|CDD|153131 cd01581, AcnB, Aconitate hydratase B catalyses the formation of
cis-aconitate from citrate as part of the TCA cycle.
Aconitase B catalytic domain. Aconitate hydratase B
catalyses the formation of cis-aconitate from citrate as
part of the TCA cycle. Aconitase has an active (4FE-4S)
and an inactive (3FE-4S) form. The active cluster is
part of the catalytic site that interconverts citrate,
cis-aconitase and isocitrate. The domain architecture of
aconitase B is different from other aconitases in that
the catalytic domain is normally found at C-terminus for
other aconitases, but it is at N-terminus for B family.
It also has a HEAT domain before domain 4 which plays a
role in protein-protein interaction. This alignment is
the core domain including domains 1,2 and 3.
Length = 436
Score = 29.8 bits (67), Expect = 1.5
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 9/84 (10%)
Query: 104 PPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNS 163
P I D+V+ A PY + LL E+ K +IL+ + + LK + +
Sbjct: 159 PGITLRDLVN---------AIPYYAIQQGLLTVEKKGKKNVFNGRILEIEGLPDLKVEQA 209
Query: 164 WPFTEDSAEDKAKSNCEDSDDEML 187
+ T+ SAE A + D E +
Sbjct: 210 FELTDASAERSAAACTVRLDKEPV 233
>gnl|CDD|225921 COG3386, COG3386, Gluconolactonase [Carbohydrate transport and
metabolism].
Length = 307
Score = 29.7 bits (67), Expect = 1.7
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 36 GNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIV 72
G +H+++ +G+K PG F + I G +I
Sbjct: 46 GGRIHRLDPETGKKRVFPSPGGFSSGALIDAGGRLIA 82
>gnl|CDD|202852 pfam04014, Antitoxin-MazE, Antidote-toxin recognition MazE. MazE
is the antidote to the toxin MazF of E. coli. MazE-MazF
in E. coli is a regulated prokaryotic chromosomal
addiction module. MazE antidote is degraded by the
ClpPA protease of the bacterial proteasome. MazE-MazF
is thought to play a role in programmed cell death when
cells suffer nutrient deprivation, and MazE-MazF
modules have also been implicated in the bacteriostatic
effects of other addiction modules. MazF toxin
functions as an mRNA interferase, cleaving mRNAs at ACA
sequences to inhibit protein synthesis leading to cell
growth arrest.
Length = 47
Score = 26.4 bits (59), Expect = 2.5
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 47 GEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEG 78
G V++P + R + IK GD V ++ +G
Sbjct: 4 GNSGAVTIPKEVRKALGIKEGDEVELEVDGDG 35
>gnl|CDD|198034 smart00966, SpoVT_AbrB, SpoVT / AbrB like domain. This domain is
found in AbrB from Bacillus subtilis. The product of
the abrB gene is an ambiactive repressor and activator
of the transcription of genes expressed during the
transition state between vegetative growth and the
onset of stationary phase and sporulation. AbrB is
thought to interact directly with the transcription
initiation regions of genes under its control. AbrB
contains a helix-turn-helix structure, but this domain
ends before the helix-turn-helix begins. The product of
the B. subtilis gene spoVT is another member of this
family and is also a transcriptional regulator.
DNA-binding activity in this AbrB homologue requires
hexamerisation. Another family member has been isolated
from the Sulfolobus solfataricus and has been
identified as a homologue of bacterial repressor-like
proteins. The Escherichia coli family member SohA or
Prl1F appears to be bifunctional and is able to
regulate its own expression as well as relieve the
export block imposed by high-level synthesis of
beta-galactosidase hybrid proteins.
Length = 45
Score = 25.9 bits (58), Expect = 3.3
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 47 GEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKA 83
G V++P + R + IK GD V ++ +G ++
Sbjct: 4 GNSGQVTIPKEVREKLGIKEGDEVELEVDGDGIILEP 40
>gnl|CDD|133040 cd04197, eIF-2B_epsilon_N, The N-terminal domain of epsilon subunit
of the eIF-2B is a subfamily of glycosyltransferase 2.
N-terminal domain of epsilon subunit of the eukaryotic
translation initiation factor 2B (eIF-2B): eIF-2B is a
guanine nucleotide-exchange factor which mediates the
exchange of GDP (bound to initiation factor eIF2) for
GTP, generating active eIF2.GTP complex. EIF2B is a
complex multimeric protein consisting of five subunits
named alpha, beta, gamma, delta and epsilon. Subunit
epsilon shares sequence similarity with gamma subunit,
and with a family of bifunctional nucleotide-binding
enzymes such as ADP-glucose pyrophosphorylase,
suggesting that epsilon subunit may play roles in
nucleotide binding activity. In yeast, eIF2B gamma
enhances the activity of eIF2B-epsilon leading to the
idea that these subunits form the catalytic subcomplex.
Length = 217
Score = 28.3 bits (64), Expect = 3.4
Identities = 16/81 (19%), Positives = 26/81 (32%), Gaps = 21/81 (25%)
Query: 184 DEMLNGNLNRR----NNVMTEF------SNRTKSGQFSTVIW----------YWYLRYIK 223
E+L + RR N +MT +RT+ VI Y L
Sbjct: 121 KEILEEHKERRKKDKNAIMTMVLKEASPPHRTRRTGEEFVIAVDPKTSRLLHYEELP-GS 179
Query: 224 HRCNKKFLELEIFYGHPKCEV 244
+ L E+ + + E+
Sbjct: 180 KYRSITDLPSELLGSNSEVEI 200
>gnl|CDD|238797 cd01556, EPSP_synthase, EPSP synthase domain. 3-phosphoshikimate
1-carboxyvinyltransferase
(5-enolpyruvylshikimate-3-phosphate synthase) (EC
2.5.1.19) catalyses the reaction between
shikimate-3-phosphate (S3P) and phosphoenolpyruvate
(PEP) to form 5-enolpyruvylshkimate-3-phosphate (EPSP),
an intermediate in the shikimate pathway leading to
aromatic amino acid biosynthesis. The reaction is
phosphoenolpyruvate + 3-phosphoshikimate = phosphate +
5-O-(1-carboxyvinyl)-3-phosphoshikimate. It is found in
bacteria and plants but not animals. The enzyme is the
target of the widely used herbicide glyphosate, which
has been shown to occupy the active site. In bacteria
and plants, it is a single domain protein, while in
fungi, the domain is found as part of a multidomain
protein with functions that are all part of the
shikimate pathway.
Length = 409
Score = 28.3 bits (64), Expect = 4.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 117 EIGEQQAKPYRDLTLHLLNK 136
IGE ++KPY D T +L
Sbjct: 176 IIGELESKPYIDHTERMLRA 195
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 28.1 bits (63), Expect = 5.1
Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 14/99 (14%)
Query: 3 KATKRKHVQKELLSQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNI 62
K + + L +Y + ED +IV I+ +G+N +
Sbjct: 116 KLDNKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEV--------HLPEGP 167
Query: 63 WIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQL 101
+ P D+V +P + +I +I+ +K I + K+++
Sbjct: 168 FRYPEDYVTDQPD------RFKISEIIREKIIRYTKEEI 200
>gnl|CDD|233416 TIGR01445, intein_Nterm, intein N-terminal splicing region. This
model is based on interated search results, starting
with a curated collection of intein N-terminal splicing
regions from InBase, the New England Biolabs Intein
Database, as presented on its web site. It is designed
to recognize inteins but not the related region of the
sonic hedgehog protein.
Length = 81
Score = 26.5 bits (59), Expect = 5.1
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 212 TVIWYWYLRYIKHRCNKKFLELEIFYGHPKCEVEVITKSHQFIT 255
++ + K R K + ++ G E++ T H F+T
Sbjct: 42 KIVKARPVVVWKRRGEGKLIRIKTENGR---EIKA-TPDHPFLT 81
>gnl|CDD|234516 TIGR04236, seadorna_VP2, seadornavirus VP2 protein. This protein
family occurs in the seadornavirus virus group, with the
designation VP2 in Banna virus, Kadipiro virus, and Liao
ning virus.
Length = 953
Score = 28.3 bits (63), Expect = 5.4
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 64 IKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQLKLPPIEN 108
IKP +F I E GN KAE E I++ Y ++K L PI +
Sbjct: 883 IKPIEFYIY--FENGNDKKAEYEDIMNVSYRLYIKTPPNLLPISD 925
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 28.0 bits (63), Expect = 5.7
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 216 YWYLRYIKHRCNKKFLELEIFYGHPKCEVEVITKS 250
+L I + L F + E+E +T S
Sbjct: 371 LPFLSIIFKHNPELAARLAAFLELTEEEIEFLTGS 405
>gnl|CDD|185558 PTZ00329, PTZ00329, eukaryotic translation initiation factor 1A;
Provisional.
Length = 155
Score = 27.5 bits (61), Expect = 5.9
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 47 GEKYFVSMPGKFRNNIWIKPGDFVIV 72
G K + GK R +WI GD ++V
Sbjct: 54 GVKRLCHIRGKMRKRVWINIGDIILV 79
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 27.9 bits (63), Expect = 6.3
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 65 KPGDFVIVKPIEEGNKVKAEIEQILD 90
K GD V + +EE +++ ++E+ILD
Sbjct: 376 KNGDVVRIDDVEEAKEIRDDVEEILD 401
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 28.0 bits (63), Expect = 7.2
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 120 EQQAKPYRDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQ 160
E QA+ D+ L L E K++ E +++L+ I+ L+
Sbjct: 410 EIQAQAILDMRLQRLTGLEREKLQEEYKELLEL--IADLED 448
Score = 27.7 bits (62), Expect = 9.6
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 77 EGNKVKAEIEQILDKKYISFLKQQLKLPPIENGDIVHHFQEIGEQQAKPYR 127
E K++ E +++L+ I+ L+ L I +EI EQ P R
Sbjct: 428 EREKLQEEYKELLEL--IADLEDILASEERVLEIIREELEEIKEQFGDPRR 476
>gnl|CDD|215240 PLN02439, PLN02439, arginine decarboxylase.
Length = 559
Score = 27.7 bits (62), Expect = 7.4
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 30 KITQNSGNN----LHQIENHSGEKYFVSM 54
KI + G LH++E + G Y++ M
Sbjct: 435 KIDKFIGGEGSLPLHELEKNGGGPYYLGM 463
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 27.3 bits (61), Expect = 8.1
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 93 YISFLKQQLKLPPIENGDI 111
I+ +KQ +++P I NGDI
Sbjct: 183 IIARVKQAVRIPVIGNGDI 201
>gnl|CDD|238101 cd00172, SERPIN, SERine Proteinase INhibitors (serpins) exhibit
conformational polymorphism shifting from native to
cleaved, latent, delta, or polymorphic forms. Many
serpins, such as antitrypsin and antichymotrypsin,
function as serine protease inhibitors which regulate
blood coagulation cascades. Non-inhibitory serpins
perform many diverse functions such as chaperoning
proteins or transporting hormones. Serpins are of
medical interest because mutants have been associated
with blood clotting disorders, emphysema, cirrhosis, and
dementia.
Length = 364
Score = 27.6 bits (62), Expect = 8.3
Identities = 14/69 (20%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 97 LKQQLKLPPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNK---EEGNKVKAEIEQILDKK 153
L++ L LP +++ D+ F+ + + + L L N+ ++G VK + + K
Sbjct: 48 LRKVLGLPSLDDEDVHQAFKSLLSSLKDSEKGVELKLANRLFVQKGLTVKEDFLDLAKKY 107
Query: 154 YISFLKQQN 162
Y + ++ +
Sbjct: 108 YDAEVESVD 116
>gnl|CDD|223978 COG1049, AcnB, Aconitase B [Energy production and conversion].
Length = 852
Score = 27.8 bits (62), Expect = 8.9
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 104 PPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNS 163
P I D+VH A PY + LL E+ K +IL+ + + LK + +
Sbjct: 533 PGITLRDLVH---------AIPYYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQA 583
Query: 164 WPFTEDSAEDKAKSNCEDSDDE 185
+ T+ SAE A + E
Sbjct: 584 FELTDASAERSAAGCTIKLNKE 605
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
0.316 0.133 0.390
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: 13,838,227
Number of extensions: 1319280
Number of successful extensions: 1622
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1618
Number of HSP's successfully gapped: 70
Length of query: 275
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 179
Effective length of database: 6,679,618
Effective search space: 1195651622
Effective search space used: 1195651622
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 (21.6 bits)
S2: 58 (25.9 bits)