RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781083|ref|YP_003065496.1| hypothetical protein
CLIBASIA_04925 [Candidatus Liberibacter asiaticus str. psy62]
(160 letters)
>gnl|CDD|145066 pfam01717, Meth_synt_2, Cobalamin-independent synthase, Catalytic
domain. This is a family of vitamin-B12 independent
methionine synthases or
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferases, EC:2.1.1.14 from bacteria and
plants. Plants are the only higher eukaryotes that have
the required enzymes for methionine synthesis. This
enzyme catalyses the last step in the production of
methionine by transferring a methyl group from
5-methyltetrahydrofolate to homocysteine. The aligned
region makes up the carboxy region of the approximately
750 amino acid protein except in some hypothetical
archaeal proteins present in the family, where this
region corresponds to the entire length. This domain
contains the catalytic residues of the enzyme.
Length = 324
Score = 30.4 bits (69), Expect = 0.24
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 17/65 (26%)
Query: 68 SERGDIINALDQDLQDVESIEVFEYLKTRLSDLEAHRRSMSF--YFAK--YPKKVGPSVI 123
S+ DI++A+D DV +E R M + Y K VG V+
Sbjct: 220 SDFNDILDAIDALDVDV-------------LTIEFARSDMENLEALEEWGYGKGVGFGVV 266
Query: 124 DVVYP 128
D+ P
Sbjct: 267 DIHSP 271
>gnl|CDD|146845 pfam04409, DUF530, Protein of unknown function (DUF530). Family of
hypothetical archaeal proteins.
Length = 512
Score = 28.4 bits (63), Expect = 0.83
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 72 DIINALDQDLQDVES-IEVFEYLKTRLSDLEAHRRSMSFYFAKYP 115
DI + L+D + I+++ L++ L L+ M P
Sbjct: 16 DISIDIGDLLKDFDGFIKIYLTLESNLEILQELEEKMERRGFDGP 60
>gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 428
Score = 27.5 bits (62), Expect = 1.9
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 11/37 (29%)
Query: 26 VQRK----SFADVHEALERYKKVARVVG-------PH 51
VQR+ F ++YKKVAR+VG PH
Sbjct: 13 VQRRILYAMFELGLNLDKKYKKVARLVGDVMGKYHPH 49
>gnl|CDD|48146 cd03311, CIMS_C_terminal_like, CIMS - Cobalamine-independent
methonine synthase, or MetE, C-terminal domain_like.
Many members have been characterized as
5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers the C-terminal barrel, and a few
single-barrel sequences most similar to the C-terminal
barrel. It is assumed that the homologous N-terminal
barrel has evolved from the C-terminus via gene
duplication and has subsequently lost binding sites, and
it seems as if the two barrels forming the active enzyme
may sometimes reside on different polypeptides. The
C-terminal domain incorporates the Zinc ion, which binds
and activates homocysteine. Sidechains from both barrels
contribute to the binding of the folate substrate..
Length = 332
Score = 27.1 bits (60), Expect = 2.3
Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 9/55 (16%)
Query: 71 GDIINALDQDLQDVESIEVFEYLKTRLSDLEAHRRSMSFYFAKYPKKVGPSVIDV 125
I + + DV EY +R LE Y KKVG V+DV
Sbjct: 231 EPIAEYIFELDVDVFF---LEYDNSRAGGLEP------LKELPYDKKVGLGVVDV 276
>gnl|CDD|133181 cd05050, PTKc_Musk, Catalytic domain of the Protein Tyrosine
Kinase, Muscle-specific kinase. Protein Tyrosine Kinase
(PTK) family; Muscle-specific kinase (Musk); catalytic
(c) domain. The PTKc family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
Musk is a receptor tyr kinase (RTK) containing an
extracellular region with four immunoglobulin-like
domains and a cysteine-rich cluster, a transmembrane
segment, and an intracellular catalytic domain. Musk is
expressed and concentrated in the postsynaptic membrane
in skeletal muscle. It is essential for the
establishment of the neuromuscular junction (NMJ), a
peripheral synapse that conveys signals from motor
neurons to muscle cells. Agrin, a large proteoglycan
released from motor neurons, stimulates Musk
autophosphorylation and activation, leading to the
clustering of acetylcholine receptors (AChRs). To date,
there is no evidence to suggest that agrin binds
directly to Musk. Mutations in AChR, Musk and other
partners are responsible for diseases of the NMJ, such
as the autoimmune syndrome myasthenia gravis.
Length = 288
Score = 27.1 bits (60), Expect = 2.5
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 16 ILVFCFVSHFVQRKSFADVHEALER 40
++ C+ R SFA ++ L+R
Sbjct: 264 LMRLCWSKLPSDRPSFASINRILQR 288
>gnl|CDD|30965 COG0620, MetE, Methionine synthase II (cobalamin-independent)
[Amino acid transport and metabolism].
Length = 330
Score = 26.8 bits (59), Expect = 3.0
Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 12/93 (12%)
Query: 36 EALERYKKVARVVGPHIPNSNVFSSSVRRTYWSERGDIINALDQDLQDVESIEVFEYLKT 95
+ LE + + + + + +++ D I ALD D + E ++
Sbjct: 193 DYLEWAVEAINLAAAGVGADTQIHLHICYSEFNDIPDAIEALDAD------VIDIETSRS 246
Query: 96 RLSDLEAHRRSMSFYFAKYPKKVGPSVIDVVYP 128
R+ LE KY K++G V+D+ P
Sbjct: 247 RMELLEV------LEEVKYDKEIGLGVVDIHSP 273
>gnl|CDD|30914 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit
(sigma70/sigma32) [Transcription].
Length = 342
Score = 26.5 bits (58), Expect = 3.9
Identities = 8/51 (15%), Positives = 18/51 (35%)
Query: 67 WSERGDIINALDQDLQDVESIEVFEYLKTRLSDLEAHRRSMSFYFAKYPKK 117
+ E ++ D ++ ++ E L L++ E + F K
Sbjct: 250 FLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPK 300
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-1 binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 25.6 bits (56), Expect = 6.1
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 3 YLSVTWNDLVQVSILVFCFVSHFVQRKSFADVHEALE 39
Y+ +W LV V FC ++H+ + D A E
Sbjct: 227 YVPFSWTALVHVKAEHFCALAHYHAAMALCDSSPASE 263
>gnl|CDD|33013 COG3200, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP)
synthase [Amino acid transport and metabolism].
Length = 445
Score = 25.7 bits (56), Expect = 6.2
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 43 KVARVVGPHI-PNSNVFSSSVRRTYWSERGDIINALDQD 80
KV R+ G P S+ T S RGDIIN ++ D
Sbjct: 105 KVGRIAGQFAKPRSSDHEQLGGVTLPSYRGDIINGIEFD 143
>gnl|CDD|36398 KOG1184, KOG1184, KOG1184, Thiamine pyrophosphate-requiring enzyme
[Amino acid transport and metabolism, Coenzyme transport
and metabolism].
Length = 561
Score = 25.2 bits (55), Expect = 8.0
Identities = 7/65 (10%), Positives = 21/65 (32%)
Query: 85 ESIEVFEYLKTRLSDLEAHRRSMSFYFAKYPKKVGPSVIDVVYPHSHLVKEDKVDEKNSS 144
++ F + ++ + M + + K++ + V E K +
Sbjct: 305 KNAIEFHSDRVKIRNATFGGVLMKDFLQELAKRIKKNKTSYENYVRIPVPEPKPLACPPN 364
Query: 145 SELKV 149
+ L+
Sbjct: 365 APLRQ 369
>gnl|CDD|36244 KOG1026, KOG1026, KOG1026, Nerve growth factor receptor TRKA and
related tyrosine kinases [Signal transduction
mechanisms, Intracellular trafficking, secretion, and
vesicular transport].
Length = 774
Score = 25.3 bits (55), Expect = 8.1
Identities = 7/26 (26%), Positives = 16/26 (61%)
Query: 15 SILVFCFVSHFVQRKSFADVHEALER 40
S+++ C+ + +R SF ++H L+
Sbjct: 736 SLMLECWNENPKRRPSFKEIHSRLQA 761
>gnl|CDD|153133 cd01583, IPMI, 3-isopropylmalate dehydratase catalyzes the
isomerization between 2-isopropylmalate and
3-isopropylmalate. Aconatase-like catalytic domain of
3-isopropylmalate dehydratase and related
uncharacterized proteins. 3-isopropylmalate dehydratase
catalyzes the isomerization between 2-isopropylmalate
and 3-isopropylmalate, via the formation of
2-isopropylmaleate 3-isopropylmalate. IPMI is involved
in fungal and bacterial leucine biosynthesis and is also
found in eukaryotes.
Length = 382
Score = 25.2 bits (56), Expect = 8.7
Identities = 15/47 (31%), Positives = 18/47 (38%), Gaps = 10/47 (21%)
Query: 96 RLSDLEAHRRSMSFYFAKYPK--KVGPSVIDVVYPHSHLVKEDKVDE 140
RL DL A A+ K KV V +V P S V + E
Sbjct: 273 RLEDLRA--------AAEILKGRKVADGVRLIVVPASQRVYKQAEKE 311
>gnl|CDD|144761 pfam01282, Ribosomal_S24e, Ribosomal protein S24e.
Length = 83
Score = 25.3 bits (56), Expect = 9.2
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 16 ILVFCFVSHFVQRKS--FADVHEALERYKKV 44
++VF F + F KS FA ++++LE KK
Sbjct: 33 VVVFGFKTEFGGGKSTGFALIYDSLEAAKKF 63
>gnl|CDD|114015 pfam05266, DUF724, Protein of unknown function (DUF724). This
family contains several uncharacterized proteins found
in Arabidopsis thaliana and other plants. This region is
often found associated with Agenet domains and may
contain coiled-coil.
Length = 190
Score = 25.1 bits (55), Expect = 9.7
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 9/84 (10%)
Query: 25 FVQRKSFADVHEALERYKKVARVVGPHIPNSNVFSSSVRRTYWSERG---DIINALDQ-- 79
F ++ F E++E +KKV + PH +R + G I L++
Sbjct: 5 FTKKSPFWKTFESMEVFKKVPQ--SPHFSPLLETPEDLRE--GTAVGLMVTFIGLLEEVK 60
Query: 80 DLQDVESIEVFEYLKTRLSDLEAH 103
LQ +SI FE L S+LE H
Sbjct: 61 KLQIDDSISEFESLSKCFSELEKH 84
>gnl|CDD|37897 KOG2686, KOG2686, KOG2686, Choline kinase [Cell
wall/membrane/envelope biogenesis].
Length = 366
Score = 24.9 bits (54), Expect = 9.8
Identities = 19/78 (24%), Positives = 26/78 (33%), Gaps = 13/78 (16%)
Query: 3 YLSVTWNDLVQVSILVFCFVSH---------FVQRKSFADVHEALERYKKVARVVGPHIP 53
YL W D+ I + FV S + E K + R+ G +
Sbjct: 30 YLGGAWRDV----INEEQRLEVIPGGGSNLLFVVTSSASTTPIKDEPRKVLLRIYGQGVD 85
Query: 54 NSNVFSSSVRRTYWSERG 71
S + SV SERG
Sbjct: 86 FSQRETESVMFAILSERG 103
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.133 0.386
Gapped
Lambda K H
0.267 0.0660 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,890,440
Number of extensions: 90498
Number of successful extensions: 246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 22
Length of query: 160
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 74
Effective length of database: 4,405,363
Effective search space: 325996862
Effective search space used: 325996862
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 (24.3 bits)