RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5450
(133 letters)
>gnl|CDD|176376 cd01781, AF6_RA_repeat2, Ubiquitin domain of AT-6, second repeat.
The AF-6 protein (also known as afadin and canoe) is a
multidomain cell junction protein that contains two
N-terminal Ras-associating (RA) domains in addition to
FHA (forkhead-associated), DIL (class V myosin homology
region), and PDZ domains and a proline-rich region. AF6
acts downstream of the Egfr (Epidermal Growth
Factor-receptor)/Ras signalling pathway and provides a
link from Egfr to cytoskeletal elements.
Length = 100
Score = 112 bits (282), Expect = 2e-33
Identities = 45/107 (42%), Positives = 58/107 (54%), Gaps = 9/107 (8%)
Query: 26 GGTLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPE 85
GGTLKIYG SL PYKT+LLS+ DNA ++V E L KYGL + D YCLV+V+ +
Sbjct: 1 GGTLKIYGGSLVPTRPYKTILLSINDNADRIVGEALEKYGLEKSDPDDYCLVEVSN--DD 58
Query: 86 TPNTAQQNGGDQFMNNQREYILDEDECPLAILMNHPQSRESRTIQFK 132
++ D E ILD+DECPL I+ P +
Sbjct: 59 DRKSSDLREID-------ERILDDDECPLFIMTAGPGENGFDSFLAI 98
>gnl|CDD|214612 smart00314, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Kalhammer et al. have
shown that not all RA domains bind RasGTP. Predicted
structure similar to that determined, and that of the
RasGTP-binding domain of Raf kinase. Predicted RA
domains in PLC210 and nore1 found to bind RasGTP.
Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
Length = 90
Score = 56.5 bits (137), Expect = 9e-12
Identities = 27/106 (25%), Positives = 48/106 (45%), Gaps = 21/106 (19%)
Query: 27 GTLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPET 86
L++Y + L YKTL +S R A V++++L K+ LT +D +Y LV+V
Sbjct: 3 FVLRVYVDDLP-GGTYKTLRVSSRTTARDVIQQLLEKFHLT-DDPEEYVLVEV------- 53
Query: 87 PNTAQQNGGDQFMNNQREYILDEDECPLAILMNHPQSRESRTIQFK 132
+ + +E +L +DE PL + P+ + +
Sbjct: 54 ------------LPDGKERVLPDDENPLQLQKLWPRRGPNLRFVLR 87
>gnl|CDD|176363 cd01768, RA, RA (Ras-associating) ubiquitin domain. The RA
(Ras-associating) domain is structurally similar to
ubiquitin and is present in one or two copies in a
number of signalling molecules that bind and regulate a
small GTPase called Ras or the Ras-related GTPases, Ral
and Rap. RA-containing proteins include RalGDS, AF6,
RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C
epsilon.
Length = 87
Score = 53.4 bits (129), Expect = 2e-10
Identities = 31/105 (29%), Positives = 46/105 (43%), Gaps = 20/105 (19%)
Query: 28 TLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPETP 87
L++Y E YKTL +S A V++++L K+GL +D Y LV+V
Sbjct: 1 VLRVYPEDP-SGGTYKTLRVSKDTTAQDVIQQLLKKFGLD-DDPEDYALVEV-------- 50
Query: 88 NTAQQNGGDQFMNNQREYILDEDECPLAILMNHPQSRESRTIQFK 132
+ E +L DECPL I +N P+ RE +
Sbjct: 51 ----------LGDGGLERLLLPDECPLQIQLNAPRQREDLRFLLR 85
>gnl|CDD|201444 pfam00788, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Recent evidence (not
yet in MEDLINE) shows that some RA domains do NOT bind
RasGTP. Predicted structure similar to that determined,
and that of the RasGTP-binding domain of Raf kinase.
Length = 87
Score = 53.1 bits (128), Expect = 2e-10
Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 21/100 (21%)
Query: 28 TLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPETP 87
L++Y E YKT+L+S A +V++ L K+GL +D Y LV +
Sbjct: 1 VLRVYTEDGTPGT-YKTILVSSTTTAQEVIRAALKKFGLA-DDPEDYVLVVLE------- 51
Query: 88 NTAQQNGGDQFMNNQREYILDEDECPLAILMNHPQSRESR 127
E +L +DE PL I + P SR
Sbjct: 52 ------------RGGEERVLPDDEKPLQIQLQLPGDASSR 79
>gnl|CDD|176351 cd00153, RalGDS_RA, Ubiquitin domain of RalGDS-like factor (RLF)
and related proteins. This CD represents the
C-terminal Ras-associating (RA) domain of three closely
related guanine-nucleotide exchange factors (GEF's),
Ral guanine nucleotide dissociation stimulator
(RalGDS), RalGDS-like (RGL), and RalGDS-like factor
(RLF). The RalGDS proteins are downstream effectors of
the Ras-related protein Ral, providing a mechanism for
Ral activation by extracellular signals. The RA domain
is structurally similar to ubiquitin and exists in a
number of other signalling proteins including AF6,
rasfadin, SNX27, CYR1, and STE50.
Length = 87
Score = 34.3 bits (79), Expect = 0.003
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 42 YKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQV 79
YK++LL+ +D A QV++ + K+ L E A Y LVQV
Sbjct: 18 YKSILLTSQDKAPQVIRRAMEKHNLESEVAEDYELVQV 55
>gnl|CDD|175983 cd04016, C2_Tollip, C2 domain present in Toll-interacting protein
(Tollip). Tollip is a part of the Interleukin-1
receptor (IL-1R) signaling pathway. Tollip is proposed
to link serine/threonine kinase IRAK to IL-1Rs as well
as inhibiting phosphorylation of IRAK. There is a
single C2 domain present in Tollip. C2 domains fold
into an 8-standed beta-sandwich that can adopt 2
structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions.
Length = 121
Score = 32.7 bits (75), Expect = 0.017
Identities = 21/41 (51%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 56 VVKEMLAK-YGLTREDAHQYCLVQVNTAIPETPNTAQQNGG 95
VV+ L K YGLTR D YC ++V A+ ETP TA NG
Sbjct: 8 VVQAKLVKNYGLTRMDP--YCRIRVGHAVYETP-TA-YNGA 44
>gnl|CDD|237245 PRK12879, PRK12879, 3-oxoacyl-(acyl carrier protein) synthase
III; Reviewed.
Length = 325
Score = 32.5 bits (75), Expect = 0.043
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 51 DNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPE--TPNTAQQ 92
D A + + LA+ GL ED L+ V T P+ P+TA Q
Sbjct: 55 DLAIKAAERALARAGLDAEDID---LIIVATTTPDYLFPSTASQ 95
>gnl|CDD|223094 COG0015, PurB, Adenylosuccinate lyase [Nucleotide transport and
metabolism].
Length = 438
Score = 31.4 bits (72), Expect = 0.091
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 53 ATQVVKEMLAKYGLTREDAHQYCLVQVNTAI 83
A++ V L K G+ RE+AH+ LV+
Sbjct: 360 ASERVMLALRKKGMGREEAHE--LVREKAMK 388
>gnl|CDD|176378 cd01783, DAGK_delta_RA, Ubiquitin-like domain of Diacylgylcerol
kinase (DAGK). DAGK_delta_RA Diacylgylcerol kinase
(DAGK) phosphorylates the second messenger
diacylglycerol to phosphatidic acid as part of a
protein kinase C pathway. Nine mammalian DAGK isotypes
have been identified, which are classified into five
subgroups according to their domain architecture and
the DAGK-delta and -theta isozymes, which fall into one
such group, contain an RA (Ras-associated) domain.
DAGKs also contain a conserved catalytic domain
(DAGKc), an assesory domain (DAGKa), and an array of
conserved motifs that are likely to play a role in
lipid-protein and protein-protein interactions in
various DAG/PA-dependent signalling pathways.
Length = 97
Score = 30.5 bits (69), Expect = 0.095
Identities = 13/53 (24%), Positives = 25/53 (47%)
Query: 27 GTLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQV 79
+K+Y L V Y ++ ++ V+ E+L +GL E + L++V
Sbjct: 3 EVVKVYPGWLRVGVAYVSIRVNKDTTVQDVILEVLPLFGLQAECPESFRLIEV 55
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 31.2 bits (71), Expect = 0.13
Identities = 23/74 (31%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 16 FRSKDGGPDTGGTLKIYGESLCRDVPYKTLLLSVRDNA--TQVVKEMLAKYGLTREDAHQ 73
+ DGGP G L R VP K L L+ A T V +LA YG+ R
Sbjct: 436 YFGGDGGPKHDGVLL-------RGVPVKRLTLADGSTALVTTVFDLLLANYGVDRGLLDG 488
Query: 74 YCLVQVNTAIPETP 87
+ P TP
Sbjct: 489 NSAKSYDDPKPYTP 502
>gnl|CDD|176381 cd01786, STE50_RA, Ubiquitin-like domain of STE50_RA. STE50_RA
The fungal adaptor protein STE50 is an essential
component of three MAPK-mediated signalling pathways,
which control the mating response, invasive/filamentous
growth and osmotolerance (HOG pathway), respectively.
STE50 functions in cell signalling between the activated
G protein and STE11. The domain architecture of STE50
includes an amino-terminal SAM (sterile alpha motif)
domain in addition to the carboxy-terminal
ubiquitin-like RA (RAS-associated) domain. While the
SAM domain interacts with STE11, the RA domain interacts
with CDC42 and RAS. Modulation of signal transduction
by STE50 specifically affects the pheromone-response
pathway in yeast.
Length = 98
Score = 29.0 bits (65), Expect = 0.30
Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 20/79 (25%)
Query: 41 PYKTLLLSVRDNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPETPNTAQQNGGDQFMN 100
P K L S D+ +++K + ++ L +D QY LV GDQ
Sbjct: 25 PLKQLRASKEDSCEKILKNAMKRHNLNDQDWRQYVLVICY--------------GDQ--- 67
Query: 101 NQREYILDEDECPLAILMN 119
E ILD DE P+ I N
Sbjct: 68 ---ERILDLDEKPVIIFKN 83
>gnl|CDD|234355 TIGR03790, TIGR03790, TIGR03790 family protein. Despite a broad
and sporadic distribution (Cyanobacteria,
Verrucomicrobia, Acidobacteria, beta and delta
Proteobacteria, and Planctomycetes), this
uncharacterized protein family occurs only among the
roughly 8 percent of prokarotyic species that carry
homologs of the integral membrane protein exosortase
(see TIGR02602), a proposed protein-sorting system
transpeptidase.
Length = 316
Score = 28.9 bits (65), Expect = 0.64
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 3/61 (4%)
Query: 2 RRRRQQKLEQKLQQFRSKDGGPDTGGTL---KIYGESLCRDVPYKTLLLSVRDNATQVVK 58
R Q++++ L+ + ++G G +I L VP + N V
Sbjct: 45 REEFFQQIKEPLRAYLVENGWWVPSGKRLGARIRVLVLTWGVPLRVAGPGAGTNCASVDS 104
Query: 59 E 59
E
Sbjct: 105 E 105
>gnl|CDD|153086 cd01677, PFL2_DhaB_BssA, Pyruvate formate lyase 2 and related
enzymes. This family includes pyruvate formate lyase 2
(PFL2), B12-independent glycerol dehydratase (DhaB) and
the alpha subunit of benzylsuccinate synthase (BssA),
all of which have a highly conserved ten-stranded
alpha/beta barrel domain, which is similar to those of
PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide
reductase). Pyruvate formate lyase catalyzes a key step
in anaerobic glycolysis, the conversion of pyruvate and
CoenzymeA to formate and acetylCoA. DhaB catalyzes the
first step in the conversion of glycerol to
1,3-propanediol while BssA catalyzes the first step in
the anaerobic mineralization of both toluene and
m-xylene.
Length = 781
Score = 29.2 bits (66), Expect = 0.65
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 52 NATQVVKEMLAKYGLTREDAHQYCLVQ-VNTAIP 84
N V+ +L K G++ EDA Y L+ V T P
Sbjct: 401 NDEVVIPALLRK-GVSLEDARDYGLIGCVETGAP 433
>gnl|CDD|181597 PRK08963, fadI, 3-ketoacyl-CoA thiolase; Reviewed.
Length = 428
Score = 28.8 bits (65), Expect = 0.83
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 56 VVKEMLAKYGLTREDAHQYCLVQVNTAIPETPNTAQQ 92
VV E+LA+ + E Q QV +PE PN A++
Sbjct: 36 VVGELLARSEIDPELIEQLVFGQV-VQMPEAPNIARE 71
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and
archaea also match the model The seed members used to
make the model include Nitrate reductases from
Pseudomonas fluorescens (GP:11344601), E.coli and
B.subtilis. All seed members are experimentally
characterized. Some unpublished nitrate reductases, that
are shorter sequences, and probably fragments fall in
between the noise and trusted cutoffs. Pfam models
pfam00384 (Molybdopterin oxidoreductase) and
pfam01568(Molydopterin dinucleotide binding domain) will
also match the nitrate reductase, alpha subunit [Energy
metabolism, Anaerobic].
Length = 1235
Score = 28.8 bits (64), Expect = 1.1
Identities = 26/78 (33%), Positives = 32/78 (41%), Gaps = 3/78 (3%)
Query: 21 GGPDTGGTLKIYGES-LCRDVPYKTLLLSVRDNA--TQVVKEMLAKYGLTREDAHQYCLV 77
GG T K+ GE+ L R +P K L L+ A T V LA YGL R C
Sbjct: 435 GGDGTEHFNKVEGENVLLRKLPVKRLQLADGSTALVTTVFDLTLANYGLERGLGDVNCAT 494
Query: 78 QVNTAIPETPNTAQQNGG 95
+ TP +Q G
Sbjct: 495 SYDDVKAYTPAWQEQITG 512
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 27.6 bits (62), Expect = 2.1
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 47 LSVRDNATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPETPNTAQQNGG--DQFMNNQRE 104
+VR + ++E+L K GLT ED + Q N I E A++ G ++ + +
Sbjct: 220 FAVR-AMPKAIEEVLEKAGLTPEDIDWFVPHQANLRIIEA--IAKKLGIPEEKVVVTVDK 276
Query: 105 Y 105
Y
Sbjct: 277 Y 277
>gnl|CDD|220731 pfam10397, ADSL_C, Adenylosuccinate lyase C-terminus. This is
the C-terminal seven alpha helices of the structure
whose full length represents the enzyme
adenylosuccinate lyase. This sequence lies C-terminal
to the conserved motif necessary for beta-elimination
reactions, Adenylosuccinate lyase catalyzes two steps
in the synthesis of purine nucleotides: the conversion
of succinylaminoimidazole-carboxamide ribotide into
aminoimidazole-carboxamide ribotide, the eighth step of
the de novo pathway, and the formation of adenosine
monophosphate (AMP) from adenylosuccinate, the second
step in the conversion of inosine monophosphate into
AMP.
Length = 80
Score = 26.3 bits (59), Expect = 2.1
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 53 ATQVVKEMLAKYGLTREDAHQYCLVQVNTAIPETPNTAQQNGGD 96
++ V LA+ GL RE+A++ LVQ A + G D
Sbjct: 4 MSERVLLALAEKGLGREEAYE--LVQRAAM------KAWEEGRD 39
>gnl|CDD|238426 cd00830, KAS_III, Ketoacyl-acyl carrier protein synthase III
(KASIII) initiates the elongation in type II fatty acid
synthase systems. It is found in bacteria and plants.
Elongation of fatty acids in the type II systems occurs
by Claisen condensation of malonyl-acyl carrier protein
(ACP) with acyl-ACP. KASIII initiates this process by
specifically using acetyl-CoA over acyl-CoA.
Length = 320
Score = 27.5 bits (62), Expect = 2.4
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 54 TQVVKEMLAKYGLTREDAHQYCLVQVNTAI 83
+ ++E L K GLT +D + Q N I
Sbjct: 226 PESIEEALEKAGLTPDDIDWFVPHQANLRI 255
>gnl|CDD|219071 pfam06525, SoxE, Sulfocyanin (SoxE). This family consists of
several archaeal sulfocyanin (or blue copper protein)
sequences from a number of Sulfolobus species.
Length = 195
Score = 27.1 bits (60), Expect = 2.5
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 72 HQYCLVQVNTAIPETPNTAQ 91
H LVQ NT P +P+ +
Sbjct: 107 HNLNLVQNNTPTPNSPDISS 126
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 27.4 bits (62), Expect = 2.7
Identities = 10/19 (52%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 53 ATQ-VVKEMLAKYGLTRED 70
ATQ VV+ LA G +R D
Sbjct: 88 ATQMVVERQLAAEGKSRHD 106
>gnl|CDD|198066 smart00998, ADSL_C, Adenylosuccinate lyase C-terminus.
Adenylosuccinate lyase catalyses two steps in the
synthesis of purine nucleotides: the conversion of
succinylaminoimidazole-carboxamide ribotide into
aminoimidazole-carboxamide ribotide (the fifth step of
de novo IMP biosynthesis); the formation of adenosine
monophosphate (AMP) from adenylosuccinate (the final
step in the synthesis of AMP from IMP). This entry
represents the C-terminal, seven alpha-helical, domain
of adenylosuccinate lyase.
Length = 81
Score = 25.9 bits (58), Expect = 3.1
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 61 LAKYGLTREDAHQYCLVQVNT 81
L + GL RE+A++ LVQ
Sbjct: 13 LVEKGLGREEAYE--LVQRAA 31
>gnl|CDD|102340 PRK06366, PRK06366, acetyl-CoA acetyltransferase; Provisional.
Length = 388
Score = 26.9 bits (59), Expect = 3.3
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 63 KYGLTREDAHQYCLVQVNTAIPETPNTAQQNGGDQFMNNQREYILDEDE 111
KYG+TRE A +Y + AI T + +N F + LD DE
Sbjct: 171 KYGITREMADEYSVQSYERAIRATESGEFRNEIVPFND------LDRDE 213
>gnl|CDD|233084 TIGR00671, baf, pantothenate kinase, type III. This model
describes a family of proteins found in a single copy
in at least ten different early completed bacterial
genomes. The only characterized member of the family is
Bvg accessory factor (Baf), a protein required, in
addition to the regulatory operon bvgAS, for
heterologous transcription of the Bordetella pertussis
toxin operon (ptx) in E. coli [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Pantothenate and coenzyme A].
Length = 243
Score = 26.7 bits (59), Expect = 3.9
Identities = 11/59 (18%), Positives = 19/59 (32%)
Query: 6 QQKLEQKLQQFRSKDGGPDTGGTLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLAKY 64
+ Q +R T + + L K + SV T+ V+ M+ K
Sbjct: 15 LNSGNKVYQFWRLATNLMKTYDEHSEFLKELFGKSLNKAFISSVVPELTEAVRNMIPKI 73
>gnl|CDD|180279 PRK05834, PRK05834, hypothetical protein; Provisional.
Length = 194
Score = 26.5 bits (59), Expect = 4.0
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 96 DQFMNNQREYILDE-DECPLAILMN 119
+QF+ N++ I DE DE L +L +
Sbjct: 37 NQFIINKQNAIFDELDENSLIVLYD 61
>gnl|CDD|236050 PRK07564, PRK07564, phosphoglucomutase; Validated.
Length = 543
Score = 26.6 bits (60), Expect = 4.3
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 25 TGGTLKIYGESLCRDVPYKTLLLSVRDNATQVVKEMLA 62
T T KIY ES D L ++ A ++V +++A
Sbjct: 509 TETTYKIYAESFEGD----EHLHQIQKEAQEIVADLIA 542
>gnl|CDD|143510 cd06843, PLPDE_III_PvsE_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme PvsE. This subfamily is composed
of PvsE from Vibrio parahaemolyticus and similar
proteins. PvsE is a vibrioferrin biosynthesis protein
which is homologous to eukaryotic ornithine
decarboxylase (ODC) and diaminopimelate decarboxylase
(DapDC). ODC and DapDC are fold type III PLP-dependent
enzymes that contain an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain,
similar to bacterial alanine racemases. It has been
suggested that PvsE may be involved in the biosynthesis
of the polycarboxylate siderophore vibrioferrin. It may
catalyze the decarboxylation of serine to yield
ethanolamine. PvsE may require homodimer formation and
the presence of the PLP cofactor for activity.
Length = 377
Score = 26.5 bits (59), Expect = 5.7
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 68 REDAHQYCLVQVNTAIPETPNTAQQNGG--DQFMNNQREYILDEDECP--LAILMNHPQ 122
R L++VN A+P+ P++ GG F +DE + P L +L + P
Sbjct: 112 RAGRTAPVLLRVNLALPDLPSSTLTMGGQPTPFG-------IDEADLPDALELLRDLPN 163
>gnl|CDD|217142 pfam02613, Nitrate_red_del, Nitrate reductase delta subunit.
This family is the delta subunit of the nitrate
reductase enzyme, The delta subunit is not part of the
nitrate reductase enzyme but is most likely needed for
assembly of the multi-subunit enzyme complex. In the
absence of the delta subunit the core alpha beta enzyme
complex is unstable. The delta subunit is essential for
enzyme activity in vivo and in vitro. The nitrate
reductase enzyme, EC:1.7.99.4 catalyze the conversion
of nitrite to nitrate via the reduction of an acceptor.
The nitrate reductase enzyme is composed of three
subunits. Nitrate is the most widely used alternative
electron acceptor after oxygen. This family also now
contains the family TorD, a family of cytoplasmic
chaperone proteins; like many prokaryotic
molybdoenzymes, the TMAO reductase (TorA) of
Escherichia coli requires the insertion of a
bis(molybdopterin guanine dinucleotide) molybdenum
(bis(MGD)Mo) cofactor in its catalytic site to be
active and translocated to the periplasm. The TorD
chaperone increases apoTorA activation up to four-fold,
allowing maturation of most of the apoprotein.
Therefore TorD is involved in the first step of TorA
maturation to make it competent to receive the
cofactor.
Length = 133
Score = 25.7 bits (57), Expect = 5.8
Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 2/35 (5%)
Query: 41 PYKTLLLSVRDN--ATQVVKEMLAKYGLTREDAHQ 73
PY ++ L+ R A ++ GL D
Sbjct: 49 PYASVYLTGRLRGQALAELRAFYRAAGLELADGVN 83
>gnl|CDD|180595 PRK06504, PRK06504, acetyl-CoA acetyltransferase; Provisional.
Length = 390
Score = 26.2 bits (58), Expect = 6.3
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 59 EMLA-KYGLTREDAHQYCLVQVNTAIPET 86
EM+A KYGL+++ ++ L AI T
Sbjct: 160 EMMAKKYGLSKDQLDEFALQSHQRAIAAT 188
>gnl|CDD|181000 PRK07492, PRK07492, adenylosuccinate lyase; Provisional.
Length = 435
Score = 26.1 bits (58), Expect = 7.4
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 61 LAKYGLTREDAHQYCLVQVN 80
L + G++REDA Y LVQ N
Sbjct: 364 LTQAGVSREDA--YRLVQRN 381
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
0.317 0.133 0.383
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,528,985
Number of extensions: 544556
Number of successful extensions: 678
Number of sequences better than 10.0: 1
Number of HSP's gapped: 674
Number of HSP's successfully gapped: 38
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
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 (23.9 bits)