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)