RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7788
(115 letters)
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 44.0 bits (104), Expect = 3e-06
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLL---LEARQRIPPFLAELESETEKFLD 67
IGRTGR+G+ G+A +F+ + + L ++ L L + +P E +
Sbjct: 361 IGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRP 419
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 42.1 bits (99), Expect = 1e-05
Identities = 21/50 (42%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESE 61
IGRTGR+G G + TF+ + + DL +L EA+Q +PP L +L +E
Sbjct: 465 IGRTGRAGAKGASYTFLT-PDKYRLARDLVKVLREAKQPVPPELEKLSNE 513
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 33.6 bits (78), Expect = 0.013
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 12 IGRTGRSGKTGLATTFIN 29
IGRTGR+G GLA + +
Sbjct: 330 IGRTGRAGSKGLALSLVA 347
>gnl|CDD|222730 pfam14392, zf-CCHC_4, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. This particular family
is found in plant proteins.
Length = 49
Score = 28.8 bits (65), Expect = 0.12
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 75 CAYCGGLGHRITACPK 90
C +CG LGH CPK
Sbjct: 34 CFHCGRLGHSDKECPK 49
>gnl|CDD|226569 COG4084, COG4084, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 135
Score = 29.5 bits (66), Expect = 0.23
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 28 INKSNDESVLLDLKHLLLEAR--QR--IPPFLAELESETEKFLDLGGDERGCAYCGGL 81
+ DE++LL + +L + +R + P L + E+ +D+ + C+ GL
Sbjct: 10 ERYAEDENLLLRIMKWILTSYAYRRDVVHPLAELLNIDVEEVIDILSRKLDCSSLYGL 67
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 29.1 bits (66), Expect = 0.24
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 11 MIGRTGRSGKTGLATTF 27
IGR GR+G+ G A
Sbjct: 115 RIGRAGRAGQKGTAILL 131
>gnl|CDD|182854 PRK10941, PRK10941, hypothetical protein; Provisional.
Length = 269
Score = 29.6 bits (67), Expect = 0.28
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 34 ESVLLDLKHLLLEARQRIPPFLAELESETEKFLDL 68
+ V +L+ L+ AR+ I L + + EK + L
Sbjct: 32 QDVYDELERLVSLAREEISQLL-PQDEQLEKLIAL 65
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 27.0 bits (61), Expect = 0.32
Identities = 7/17 (41%), Positives = 7/17 (41%)
Query: 74 GCAYCGGLGHRITACPK 90
C CG GH CP
Sbjct: 1 KCYNCGKEGHIARDCPS 17
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 29.0 bits (65), Expect = 0.51
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 11 MIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLA 56
IGR R G+ G A F+N+ + ++ +L LL + IP LA
Sbjct: 455 QIGRASRMGEKGTAIVFVNEED-RNLFPELVALLKSSGAAIPRELA 499
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 28.8 bits (65), Expect = 0.59
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 12 IGRTGRSGKTGLATTF 27
IGRTGR+G +G + +
Sbjct: 343 IGRTGRAGASGHSISL 358
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 28.8 bits (65), Expect = 0.65
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 12 IGRTGRSGKTGLATTFI 28
IGRTGR+G+ G A + +
Sbjct: 333 IGRTGRAGRKGTAISLV 349
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved
in eukaryotic gene regulation, such as C. elegans
GLH-1. Structure is an 18-residue zinc finger.
Length = 18
Score = 26.3 bits (59), Expect = 0.65
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 73 RGCAYCGGLGHRITACPK 90
R C CG GH CP+
Sbjct: 1 RKCYNCGKEGHLARDCPE 18
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 28.2 bits (64), Expect = 0.69
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 13/59 (22%)
Query: 5 MNTMFPMI----GRTGRSGKTGLATTFINKSNDESVLL--------DLKHLLLEARQRI 51
M P+I G +G SGKT +A+T + DES+ + D HL E R +
Sbjct: 1 MMMKKPIIIGIAGGSG-SGKTTVASTIYEELGDESIAVIPQDSYYKDQSHLSFEERVKT 58
>gnl|CDD|180286 PRK05848, PRK05848, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 273
Score = 28.1 bits (63), Expect = 1.0
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 39 DLKHLLLEARQRIPPFLAELESETEKF 65
DLK + AR+ I PF A++E E E
Sbjct: 167 DLKEFIQHARKNI-PFTAKIEIECESL 192
>gnl|CDD|130919 TIGR01860, VNFD, nitrogenase vanadium-iron protein, alpha chain.
This model represents the alpha chain of the
vanadium-containing component of the vanadium-iron
nitrogenase compound I. The complex also includes a
second alpha chain, two beta chains and two delta
chains. Compount I interacts with compound II also
known as the iron-protein which transfers electrons to
compound I where the catalysis occurs [Central
intermediary metabolism, Nitrogen fixation].
Length = 461
Score = 28.0 bits (62), Expect = 1.1
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 13/49 (26%)
Query: 44 LLEARQRIPP-----FLAELESETEKFLDLGG--------DERGCAYCG 79
LLE + IP ++ E +T +FL L ERGC+YCG
Sbjct: 4 LLECDEDIPERQKHVYIKEPGEDTTEFLPLSNIATIPGSLSERGCSYCG 52
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 28.0 bits (62), Expect = 1.3
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 34 ESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLG 69
E + LK + L A + P ++ E S +K++D+G
Sbjct: 923 ERIPDHLKKIFLTAFEIEPEWIIECASRRQKWIDMG 958
>gnl|CDD|165553 PHA03296, PHA03296, envelope glycoprotein H; Provisional.
Length = 814
Score = 27.7 bits (61), Expect = 1.5
Identities = 19/84 (22%), Positives = 26/84 (30%), Gaps = 21/84 (25%)
Query: 2 SQMMNTMFPMIGRTGR----SGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE 57
S ++ + P G R S L TF N S ++ PF A
Sbjct: 636 SWILTSRPPSGGMRYRLPDTSIAANLFLTFFNASCNKE-----------------PFAAR 678
Query: 58 LESETEKFLDLGGDERGCAYCGGL 81
+ L+L G C CG
Sbjct: 679 TAKIEDGHLNLHGAAIACILCGHA 702
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 27.1 bits (60), Expect = 1.9
Identities = 10/22 (45%), Positives = 10/22 (45%)
Query: 68 LGGDERGCAYCGGLGHRITACP 89
G ER C CG GH CP
Sbjct: 48 GGRGERSCYNCGKTGHLSRECP 69
Score = 25.5 bits (56), Expect = 5.3
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 69 GGDERGCAYCGGLGHRITACP 89
G R C CGG GH CP
Sbjct: 100 GAARRACYNCGGEGHISRDCP 120
Score = 25.5 bits (56), Expect = 6.8
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 67 DLGGDERGCAYCGGLGHRITACP 89
G ++ C CG GH CP
Sbjct: 124 KRPGGDKTCYNCGQTGHLSRDCP 146
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 27.5 bits (61), Expect = 1.9
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLL 38
IGRTGR+G+ G A F+ N E LL
Sbjct: 333 IGRTGRAGRAGRALLFVE--NRERRLL 357
>gnl|CDD|219368 pfam07299, FBP, Fibronectin-binding protein (FBP). This family
consists of several bacterial fibronectin-binding
proteins which are thought to be involved in virulence
in Listeria species.
Length = 208
Score = 26.5 bits (59), Expect = 2.8
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 32 NDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 67
ND +V+ +K L +E +I EL E ++ LD
Sbjct: 25 NDRNVIKAVKALAIE---KILDLFPELSPEQKELLD 57
>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated.
Length = 280
Score = 26.4 bits (59), Expect = 3.0
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 68 LGGDERGCAY-CGGLGHRITACP 89
L G +GC+Y C GLG + ACP
Sbjct: 130 LFGGPKGCSYGCLGLGSCVAACP 152
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 26.8 bits (59), Expect = 3.1
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 26 TFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 67
+ I K + + L DL ++ + ++ I ELE E +K LD
Sbjct: 90 SHIKKHKERNTLPDLNNVDKKTKKLINKLQKELE-ELKKELD 130
>gnl|CDD|180763 PRK06937, PRK06937, type III secretion system protein; Reviewed.
Length = 204
Score = 26.2 bits (58), Expect = 3.6
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 30 KSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLG 69
++ D LL + L+ ARQR AE + E+ LG
Sbjct: 22 RAEDYQSLLSAEELVEAARQRAEEIEAEAQEVYEQQKQLG 61
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 26.4 bits (58), Expect = 3.8
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLL 38
IGRTGR+G +G++ +F D++ L
Sbjct: 423 IGRTGRAGASGVSISFA--GEDDAFQL 447
>gnl|CDD|238936 cd01977, Nitrogenase_VFe_alpha, Nitrogenase_VFe_alpha -like:
Nitrogenase VFe protein, alpha subunit like. This group
contains proteins similar to the alpha subunits of,
the VFe protein of the vanadium-dependent (V-)
nitrogenase and the FeFe protein of the iron only (Fe-)
nitrogenase Nitrogenase catalyzes the ATP-dependent
reduction of dinitrogen (N2) to ammonia. In addition to
V- and Fe- nitrogenases there is a molybdenum
(Mo)-dependent nitrogenase which is the most widespread
and best characterized of these systems. These systems
consist of component 1 (VFe protein, FeFe protein or,
MoFe protein respectively) and, component 2 (Fe
protein). MoFe is an alpha2beta2 tetramer, V-and Fe-
nitrogenases are alpha2beta2delta2 hexamers. The alpha
and beta subunits of VFe and FeFe are similar to the
alpha and beta subunits of MoFe. For MoFe each
alphabeta pair contains one P-cluster (at the alphabeta
interface) and, one molecule of iron molybdenum
cofactor (FeMoco) contained within the alpha subunit.
The Fe protein which has a practically identical
structure in all three systems, it contains a single
[4Fe-4S] cluster. Electrons are transferred from the
[4Fe-4S] cluster of the Fe protein to the P-cluster of
the MoFe and in turn to FeMoCo, the site of substrate
reduction. The V-nitrogenase requires an iron-vanadium
cofactor (FeVco), the iron only-nitrogenase an iron
only cofactor (FeFeco). These cofactors are analogous
to the FeMoco. The V-nitrogenase has P clusters
identical to those of MoFe. In addition to N2,
nitrogenase also catalyzes the reduction of a variety
of other substrates such as acetylene The
V-nitrogenase differs from the Mo-nitrogenase in that
it produces free hydrazine, as a minor product during
dinitrogen reduction and, ethane as a minor product
during acetylene reduction.
Length = 415
Score = 26.2 bits (58), Expect = 4.2
Identities = 8/8 (100%), Positives = 8/8 (100%)
Query: 72 ERGCAYCG 79
ERGCAYCG
Sbjct: 6 ERGCAYCG 13
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 26.4 bits (59), Expect = 4.3
Identities = 11/16 (68%), Positives = 12/16 (75%), Gaps = 1/16 (6%)
Query: 11 MIGRTGRSGKTGLATT 26
+IG TG SGKT LA T
Sbjct: 102 LIGPTG-SGKTLLAQT 116
>gnl|CDD|199899 cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA alpha and beta
subunits and similar proteins. Transcription factor II
A (TFIIA) is one of the general transcription factors
for RNA polymerase II. TFIIA increases the affinity of
TATA-binding protein (TBP) for DNA in order to assemble
the initiation complex. TFIIA also functions as an
activator during development and differentiation, and
is involved in transcription from TATA-less promoters.
TFIIA is composed of more than one subunit in various
organisms. Mammalian TFIIA large subunits (TFIIA alpha
and beta) and the smaller subunit (TFIIA gamma) form a
heterotrimer. TFIIA alpha and beta are encoded by a
single gene (TFIIA_alpha_beta), its protein product is
post-translationally processed and cleaved. TOA1 and
TOA2 are the two subunits of Yeast TFIIA which
correspond to Mammalian TFIIA_alpha_beta and TFIIA
gamma, respectively. TOA1 and TOA2 form a heterodimeric
protein complex. TFIIA_alpha_beta alone is sufficient
for transcription in early embryogenesis, but the
cleaved forms, TFIIA alpha and TFIIA beta, represent
the vast majority of TFIIA in most differentiated
cells. The exact functional differences between cleaved
and uncleaved forms are not yet clear. This model also
contains paralogs of the canonical TFIIA_alpha_beta,
such as the human ALF, which may be involved in
gametogenesis and early embryogenesis (and is also
subject to proteolytic cleavage).
Length = 102
Score = 25.6 bits (57), Expect = 4.5
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 27 FINKSNDESVLLDLKHL 43
F ++ DESVL +LK L
Sbjct: 20 FEDEGVDESVLQELKQL 36
>gnl|CDD|223684 COG0611, ThiL, Thiamine monophosphate kinase [Coenzyme metabolism].
Length = 317
Score = 26.1 bits (58), Expect = 5.0
Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 11 MIGRTGRSGKTGLATTFINKSNDESVLLDL--KHLLLEARQRIPPFLAELES 60
++ TG G++ + +L +HL R + LA+L S
Sbjct: 153 LVAVTGTLGRSAAGLELLLNVLGPEDEEELIERHLRPTPRVELGLALAKLAS 204
>gnl|CDD|217266 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain.
Length = 77
Score = 24.9 bits (55), Expect = 5.2
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA 47
+ +T + F+ + + +L +L+ LLEA
Sbjct: 5 LSKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEA 40
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 25.9 bits (57), Expect = 5.4
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 12 IGRTGRSGKTGLATTFINKSNDE 34
IGR+GR G+ G+A F+ + E
Sbjct: 355 IGRSGRFGRKGVAINFVTPDDIE 377
>gnl|CDD|130920 TIGR01861, ANFD, nitrogenase iron-iron protein, alpha chain.
This model represents the all-iron variant of the
nitrogenase component I alpha chain. Molybdenum-iron
and vanadium iron forms are also found. The complete
complex contains two alpha chains, two beta chains and
two delta chains. The component I associates with
component II also known as the iron protein which
serves to provide electrons for component I [Central
intermediary metabolism, Nitrogen fixation].
Length = 513
Score = 26.1 bits (57), Expect = 5.5
Identities = 8/8 (100%), Positives = 8/8 (100%)
Query: 72 ERGCAYCG 79
ERGCAYCG
Sbjct: 46 ERGCAYCG 53
>gnl|CDD|233603 TIGR01862, N2-ase-Ialpha, nitrogenase component I, alpha chain.
This model represents the alpha chain of all three
varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of
nitrogenase [Central intermediary metabolism, Nitrogen
fixation].
Length = 443
Score = 25.9 bits (57), Expect = 6.2
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 72 ERGCAYCGGLG 82
ERGCAY G G
Sbjct: 33 ERGCAYAGAKG 43
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 25.9 bits (57), Expect = 6.2
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 6/42 (14%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLL-DLKHLLLEARQRIP 52
IGRTGR+ TG A + + DE LL D++ LL ++ IP
Sbjct: 333 IGRTGRAAATGEALSLV--CVDEHKLLRDIEKLL---KKEIP 369
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 25.9 bits (56), Expect = 7.0
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 75 CAYCGGLGHRITACP 89
C CG GH I CP
Sbjct: 179 CYRCGQKGHWIQNCP 193
>gnl|CDD|215168 PLN02299, PLN02299, 1-aminocyclopropane-1-carboxylate oxidase.
Length = 321
Score = 25.5 bits (56), Expect = 7.2
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 25 TTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDL 68
+TF + ES L D+ L E R+ + F ELE E+ LDL
Sbjct: 91 STFFLRHLPESNLADIPDLDDEYRKVMKDFALELEKLAEELLDL 134
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 25.6 bits (57), Expect = 7.7
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 13 GRTGRSGKTGLATTFINKS--NDESVLL 38
G TG +GKT LA+ F + E LL
Sbjct: 280 GATG-TGKTLLASKFAEAACRRGERCLL 306
>gnl|CDD|214941 smart00963, SRP54_N, SRP54-type protein, helical bundle domain.
This entry represents the N-terminal helical bundle
domain of the 54 kDa SRP54 component, a GTP-binding
protein that interacts with the signal sequence when it
emerges from the ribosome. SRP54 of the signal
recognition particle has a three-domain structure: an
N-terminal helical bundle domain, a GTPase domain, and
the M-domain that binds the 7s RNA and also binds the
signal sequence. The extreme C-terminal region is
glycine-rich and lower in complexity and poorly
conserved between species.
Length = 77
Score = 24.4 bits (54), Expect = 7.9
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 20 KTGLATTFINKSNDESVLLDLKHLLLEA 47
L F+ + +DE +L +L+ LLEA
Sbjct: 6 GKLLGELFLTEKDDEELLEELEEALLEA 33
>gnl|CDD|188127 TIGR01284, alt_nitrog_alph, nitrogenase alpha chain. This model
represents the alpha chains of various forms of the
nitrogen-fixing enzyme nitrogenase: vanadium-iron,
iron-iron, and molybdenum-iron. Most examples of NifD,
the molybdenum-iron type nitrogenase alpha chain, are
excluded from this model and described instead by
equivalog model TIGR01282. It appears by phylogenetic
and UPGMA trees that this model represents a distinct
clade of NifD homologs, in which arose several
molybdenum-independent forms [Central intermediary
metabolism, Nitrogen fixation].
Length = 457
Score = 25.2 bits (55), Expect = 9.2
Identities = 7/8 (87%), Positives = 8/8 (100%)
Query: 72 ERGCAYCG 79
ERGCA+CG
Sbjct: 43 ERGCAFCG 50
>gnl|CDD|99993 cd03823, GT1_ExpE7_like, This family is most closely related to the
GT1 family of glycosyltransferases. ExpE7 in
Sinorhizobium meliloti has been shown to be involved in
the biosynthesis of galactoglucans (exopolysaccharide
II).
Length = 359
Score = 25.3 bits (56), Expect = 9.2
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 42 HLLLEARQRIPPFLAELE------SETEKFLDLGGDER 73
LLLEA +R+P EL E+ +L GD R
Sbjct: 207 DLLLEAFKRLPRGDIELVIVGNGLELEEESYELEGDPR 244
>gnl|CDD|193561 cd08013, M20_ArgE_DapE_like3, 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. This group includes the
hypothetical protein ygeY from Escherichia coli, a
putative deacetylase, but many in this subfamily are
classified as unassigned peptidases. 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 fungal and bacterial, and have been
inferred by homology as being related to both ArgE and
DapE.
Length = 377
Score = 25.4 bits (56), Expect = 9.9
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 32 NDESVLLDLKHLLLEARQRIPPFLAELE 59
+E V +L+ +L + P F AE
Sbjct: 260 TEEDVEAELQAILGKLAAEDPDFKAEAR 287
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 0.134 0.388
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,577,734
Number of extensions: 470389
Number of successful extensions: 523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 522
Number of HSP's successfully gapped: 48
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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: 53 (24.0 bits)