RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780421|ref|YP_003064834.1| hypothetical protein
CLIBASIA_01530 [Candidatus Liberibacter asiaticus str. psy62]
(218 letters)
>gnl|CDD|34268 COG4649, COG4649, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 221
Score = 121 bits (305), Expect = 1e-28
Identities = 64/190 (33%), Positives = 100/190 (52%), Gaps = 1/190 (0%)
Query: 23 WIAPLLILMILSLAIWFYLFDGSHEKKKNIVGENFAQALELFNSNKLDDARSSFEKILSQ 82
+ + IL++L A + + + + G+ F AL+L NK DDA ++F +
Sbjct: 29 AVIGIAILVVLGTAGY-VGYTYWQTSRASKSGDAFLAALKLAQENKTDDALAAFTDLEKT 87
Query: 83 DNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLAPLAVRYAATLQAASILVDTSS 142
Y L+ M A++L KGDT A F ++A D P R A L+AA +LVD S
Sbjct: 88 GYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGS 147
Query: 143 YEEISKILQKLSEPSNPMHQFANEILGISALKFGKVQKAKTIFEELAKDNNSPFGISTRS 202
Y+++S ++ L+ NPM A E LG++A K G KAK+ F ++A D +P I R+
Sbjct: 148 YDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAPRNIRQRA 207
Query: 203 QMILANIIAS 212
Q++L I +S
Sbjct: 208 QIMLDLIDSS 217
>gnl|CDD|31915 COG1729, COG1729, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 262
Score = 40.0 bits (93), Expect = 5e-04
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 10/102 (9%)
Query: 57 FAQALELFNSNKLDDARSSFEKILSQ-DNKLYNPLSNMYIASILVAKGDTKNAAEIFLKV 115
+ AL+L+ S +A +F+ + + N Y P + ++ L A+GD ++AA IF +V
Sbjct: 145 YNAALDLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARV 204
Query: 116 AND----DLAPLAVRYAATLQAASILVDTSSYEEISKILQKL 153
D AP A L+ L + +E LQ++
Sbjct: 205 VKDYPKSPKAP-----DALLKLGVSLGRLGNTDEACATLQQV 241
>gnl|CDD|37216 KOG2005, KOG2005, KOG2005, 26S proteasome regulatory complex,
subunit RPN1/PSMD2 [Posttranslational modification,
protein turnover, chaperones].
Length = 878
Score = 34.1 bits (78), Expect = 0.033
Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 13/124 (10%)
Query: 84 NKLYNPLSNMYIASIL---VAKGDTKN--AAEIFLKVANDDLAPLAVRYAATLQAASILV 138
+ L + S I +IL +A ++ E+ + D +P+ V A+L I V
Sbjct: 459 DYLQSSSSIHRIGAILGLGLAYAGSQREEVLELLSPIMFDTKSPMEVVAFASLSLGMIFV 518
Query: 139 DTSSYEEISKILQKL-----SEPSNPMHQFANEILGISALKFGKVQKAKTIFEELAKDNN 193
+ + + S ILQ L +E + +F LG++ L GK Q++ E K
Sbjct: 519 GSCNEDVTSSILQTLMEKSETELEDQWFRFL--ALGLALLFLGK-QESVDAVVETIKAIE 575
Query: 194 SPFG 197
P
Sbjct: 576 GPIR 579
>gnl|CDD|113045 pfam04258, Peptidase_A22B, Signal peptide peptidase. The members
of this family are membrane proteins. In some proteins
this region is found associated with pfam02225. This
family corresponds with Merops subfamily A22B, the type
example of which is signal peptide peptidase. There is a
sequence-similarity relationship with pfam01080.
Length = 294
Score = 30.4 bits (69), Expect = 0.40
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 11 KGKCKMGKCCYKWIAPLLILMILSLAI--WFYLFDGSHEKKKNIVGENFA 58
K K K+ ++ L+ ++L + W+Y+ H ++I+G
Sbjct: 80 KKKSKLELKNGRFTYSELVALLLCIVFAVWWYVLRKEHWILQDILGIALC 129
>gnl|CDD|37287 KOG2076, KOG2076, KOG2076, RNA polymerase III transcription factor
TFIIIC [Transcription].
Length = 895
Score = 29.9 bits (67), Expect = 0.52
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 57 FAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVA 116
+A LF L++A +++ QD + + I +GD + A +L A
Sbjct: 143 LGEANNLFARGDLEEAEEILMEVIKQDPRNPIAYY--TLGEIYEQRGDIEKALNFWLLAA 200
>gnl|CDD|30564 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 28.7 bits (64), Expect = 1.3
Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 11/108 (10%)
Query: 64 FNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLA-P 122
F+ L++A+ + E+ LYN L + + D K F + +DD P
Sbjct: 306 FSEELLEEAKKALER-------LYNALRRLRDLAGDAELADLKEFEARFREALDDDFNTP 358
Query: 123 LAVRYAATLQAASILVDTSSYEEISKILQKLSEPSNPMHQFANEILGI 170
A+ A L + ++ E S LS + ++LG+
Sbjct: 359 KAL---AVLFELAKEINRLLEEGKSDAKAVLSALKALLAILGLKVLGL 403
>gnl|CDD|33593 COG3799, Mal, Methylaspartate ammonia-lyase [Amino acid transport
and metabolism].
Length = 410
Score = 28.4 bits (63), Expect = 1.4
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 87 YNPLSNMYIASILVAKGDTK--NAAEIFLKVANDDLAPLAVRYA---ATLQAASILVDTS 141
+ P N ++ +LV + + A +F K+ + +L AVRY A L AA++ T+
Sbjct: 89 FIPFLNDHVKPLLVGRDVDAFLDNARVFEKLIDGNLLHTAVRYGVSQALLDAAALATGTT 148
Query: 142 SYEEISKILQKLSEPSNPMHQF 163
E + Q L + + F
Sbjct: 149 KTEVVCDEWQ-LPRVTESVPLF 169
>gnl|CDD|113791 pfam05034, MAAL_N, Methylaspartate ammonia-lyase N-terminus.
Methylaspartate ammonia-lyase EC:4.3.1.2 catalyses the
second step of fermentation of glutamate. It is a
homodimer. This family represents the N-terminal region
of Methylaspartate ammonia-lyase. This domain is
structurally related to pfam03952. This domain is
associated with the catalytic domain pfam07476.
Length = 158
Score = 28.6 bits (64), Expect = 1.5
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 89 PLSNMYIASILVAKGDT--KNAAEIFLKVANDDLAPLAVRYA---ATLQAASILVDTSSY 143
P++ +A L+ + + + A K+ + + A+RY A L AA+ T+
Sbjct: 90 PVTERVVAPRLIGRDVSRFLDNAAKVDKLIDGNRLHTAIRYGVSQALLDAAAHARRTTMA 149
Query: 144 E 144
E
Sbjct: 150 E 150
>gnl|CDD|143395 cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase
superfamily. The aldehyde dehydrogenase superfamily
(ALDH-SF) of NAD(P)+-dependent enzymes, in general,
oxidize a wide range of endogenous and exogenous
aliphatic and aromatic aldehydes to their corresponding
carboxylic acids and play an important role in
detoxification. Besides aldehyde detoxification, many
ALDH isozymes possess multiple additional catalytic and
non-catalytic functions such as participating in
metabolic pathways, or as binding proteins, or
osmoregulants, to mention a few. The enzyme has three
domains, a NAD(P)+ cofactor-binding domain, a catalytic
domain, and a bridging domain; and the active enzyme is
generally either homodimeric or homotetrameric. The
catalytic mechanism is proposed to involve cofactor
binding, resulting in a conformational change and
activation of an invariant catalytic cysteine
nucleophile. The cysteine and aldehyde substrate form an
oxyanion thiohemiacetal intermediate resulting in
hydride transfer to the cofactor and formation of a
thioacylenzyme intermediate. Hydrolysis of the
thioacylenzyme and release of the carboxylic acid
product occurs, and in most cases, the reduced cofactor
dissociates from the enzyme. The evolutionary
phylogenetic tree of ALDHs appears to have an initial
bifurcation between what has been characterized as the
classical aldehyde dehydrogenases, the ALDH family
(ALDH) and extended family members or aldehyde
dehydrogenase-like (ALDH-L) proteins. The ALDH proteins
are represented by enzymes which share a number of
highly conserved residues necessary for catalysis and
cofactor binding and they include such proteins as
retinal dehydrogenase, 10-formyltetrahydrofolate
dehydrogenase, non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase,
delta(1)-pyrroline-5-carboxylate dehydrogenases,
alpha-ketoglutaric semialdehyde dehydrogenase,
alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
aldehyde dehydrogenase and succinate-semialdehyde
dehydrogenase. Included in this larger group are all
human, Arabidopsis, Tortula, fungal, protozoan, and
Drosophila ALDHs identified in families ALDH1 through
ALDH22 with the exception of families ALDH18, ALDH19,
and ALDH20 which are present in the ALDH-like group. The
ALDH-like group is represented by such proteins as
gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA
reductase, and coenzyme A acylating aldehyde
dehydrogenase. All of these proteins have a conserved
cysteine that aligns with the catalytic cysteine of the
ALDH group.
Length = 367
Score = 27.2 bits (61), Expect = 3.8
Identities = 27/105 (25%), Positives = 43/105 (40%), Gaps = 19/105 (18%)
Query: 106 KNAAEIFLKVANDDLAPLAVRYAATLQ------AAS-ILVDTSSYEEISKILQKLSEPSN 158
K+ I + A+ D A + A AAS +LV S Y+E + L + +
Sbjct: 205 KSPV-IVDEDADLDAAVEGAVFGAFFNAGQICTAASRLLVHESIYDEFVEKLVTVLVDVD 263
Query: 159 PMHQFAN-EILGISALKFGKVQ---KAKTIFEELAKDNNSPFGIS 199
P A EI FG V + K E +A N++ +G++
Sbjct: 264 PDMPIAQEEI-------FGPVLPVIRFKDEEEAIALANDTEYGLT 301
>gnl|CDD|37213 KOG2002, KOG2002, KOG2002, TPR-containing nuclear phosphoprotein
that regulates K(+) uptake [Inorganic ion transport and
metabolism].
Length = 1018
Score = 26.9 bits (59), Expect = 4.2
Identities = 20/135 (14%), Positives = 50/135 (37%), Gaps = 3/135 (2%)
Query: 60 ALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDD 119
L +S+ ++ ++N NP++ ++A+ K D + + +
Sbjct: 243 DLNFNDSDSYKKGVQLLQRAYKENN--ENPVALNHLANHFYFKKDYERVWHLAEHAIKNT 300
Query: 120 LAPLAVRYAATLQAASILVDTSSYEEISKILQKLSEPSNPMHQFANEILGISALKFGKVQ 179
+++ + Q +E+ K + + N LG +K G ++
Sbjct: 301 ENK-SIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGLGQMYIKRGDLE 359
Query: 180 KAKTIFEELAKDNNS 194
++K FE++ K +
Sbjct: 360 ESKFCFEKVLKQLPN 374
>gnl|CDD|37035 KOG1824, KOG1824, KOG1824, TATA-binding protein-interacting protein
[General function prediction only].
Length = 1233
Score = 26.5 bits (58), Expect = 5.6
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 126 RYAAT------LQAASILVDTSSYEEISK-ILQKLSEPSNPMHQFANEILGISALKFGKV 178
R+ AT LQ SI +D S ++ K +L+ L + + + A + LG K +
Sbjct: 22 RFMATSDLMTELQKDSIKLDDDSERKVVKMLLKLLEDKNGEVQNLAVKCLGPLVSKVKE- 80
Query: 179 QKAKTIFEEL 188
+ +TI E L
Sbjct: 81 DQLETIVENL 90
>gnl|CDD|37214 KOG2003, KOG2003, KOG2003, TPR repeat-containing protein [General
function prediction only].
Length = 840
Score = 26.6 bits (58), Expect = 5.9
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 2/79 (2%)
Query: 41 LFDGSHEKKKNIVGENFAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILV 100
+F+ K + N L DA+ + L+ D YN + +I
Sbjct: 444 VFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDR--YNAAALTNKGNIAF 501
Query: 101 AKGDTKNAAEIFLKVANDD 119
A GD AAE + + N+D
Sbjct: 502 ANGDLDKAAEFYKEALNND 520
>gnl|CDD|143422 cd07104, ALDH_BenzADH-like, ALDH subfamily: NAD(P)+-dependent
benzaldehyde dehydrogenase II, vanillin dehydrogenase,
p-hydroxybenzaldehyde dehydrogenase and related
proteins. ALDH subfamily which includes the
NAD(P)+-dependent, benzaldehyde dehydrogenase II (XylC,
BenzADH, EC=1.2.1.28) involved in the oxidation of
benzyl alcohol to benzoate; p-hydroxybenzaldehyde
dehydrogenase (PchA, HBenzADH) which catalyzes the
oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic
acid; vanillin dehydrogenase (Vdh, VaniDH) involved in
the metabolism of ferulic acid as seen in Pseudomonas
putida KT2440; and other related sequences.
Length = 431
Score = 26.0 bits (58), Expect = 9.3
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 17/64 (26%)
Query: 153 LSEPSNPMHQFANEILGISALKFGKV---QKAKTIFEELAKDNNSPFGISTRSQMILANI 209
LS+ + M F EI FG V E + N++ +G+S A +
Sbjct: 323 LSDVTPDMPIFREEI-------FGPVAPVIPFDDDEEAVELANDTEYGLS-------AAV 368
Query: 210 IASD 213
D
Sbjct: 369 FTRD 372
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
0.316 0.131 0.364
Gapped
Lambda K H
0.267 0.0631 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,354,578
Number of extensions: 113820
Number of successful extensions: 457
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 33
Length of query: 218
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,318,927
Effective search space: 552822656
Effective search space used: 552822656
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: 55 (25.2 bits)