RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781179|ref|YP_003065592.1| D-alanine--D-alanine ligase [Candidatus Liberibacter asiaticus str. psy62] (300 letters) >gnl|CDD|31374 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp enzymes [Cell envelope biogenesis, outer membrane]. Length = 317 Score = 271 bits (695), Expect = 1e-73 Identities = 117/314 (37%), Positives = 177/314 (56%), Gaps = 20/314 (6%) Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAH-------LKPDLA 54 AVL+GG S+EREVSL S KA AL+ G+ V+ +D+ + +L K D+ Sbjct: 6 AVLLGGRSAEREVSLLSAKAVLRALKGFGYDVTPVDITEAGLWMLDKEVTKRVLQKADVV 65 Query: 55 FNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVN 114 F VLHG +GEDG +Q +LELL IPY G+LASA +MDK+ +K++ + G+PV P + + Sbjct: 66 FPVLHGPYGEDGTIQGLLELLGIPYVGKGVLASAGAMDKIVTKRLFKAEGLPVAPYVALT 125 Query: 115 RFTMDSQHL------ISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLI 168 R S + + P +KP + GSS+G + + L ++ + +L Sbjct: 126 RDEYSSVIVEEVEEGLGFPLFVKPAREGSSVGRSPVNVEGD--LQSALELAFKYDRDVLR 183 Query: 169 EQYVDGIELTCGVMGD----ASLDVTEIAVPKSDFYSYELKYSSLNST-HVLPAKIPLDI 223 EQ + G E+ GV+G+ +L + EI +FY YE KY S + +PA + +I Sbjct: 184 EQGITGREIEVGVLGNDYEEQALPLGEIPPKGEEFYDYEAKYLSTGGAQYDIPAGLTDEI 243 Query: 224 YKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGY 283 ++E++ LA A++A+GC G++R DF D + LE+N PGMT +S+FP+ AA AG Sbjct: 244 HEEIKELALRAYKALGCLGLARVDFFVDDDEGEFVLLEVNTNPGMTAMSLFPKAAAAAGI 303 Query: 284 SFRELLLWMVEDAS 297 SF L+L VE A Sbjct: 304 SFAILVLRFVELAL 317 >gnl|CDD|145141 pfam01820, Dala_Dala_lig_N, D-ala D-ala ligase N-terminus. This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). Length = 110 Score = 102 bits (257), Expect = 1e-22 Identities = 44/107 (41%), Positives = 54/107 (50%), Gaps = 26/107 (24%) Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDR--------------------- 40 AVL GG SSE EVSL S +A AL+ G++V ID+D+ Sbjct: 4 AVLFGGRSSEHEVSLKSARAVLKALDKEGYEVIPIDIDKDGRWLLGDGDLGLLAPDDKLD 63 Query: 41 -----SVGLVLAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHS 82 + VL K D+ F VLHG FGEDG +Q +LELL IPY S Sbjct: 64 LEDKAELLAVLLAEKVDVVFPVLHGPFGEDGTIQGLLELLGIPYVGS 110 >gnl|CDD|30806 COG0458, CarB, Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]. Length = 400 Score = 51.4 bits (123), Expect = 3e-07 Identities = 51/225 (22%), Positives = 90/225 (40%), Gaps = 16/225 (7%) Query: 61 NFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDS 120 N + + +LE + S A ++ DK K+ + G+PV I + D Sbjct: 85 NAALELKEKGVLEKYGVEVVGSDPEAIEIAEDKKLFKEAMREIGIPVPSRIAHSVEEADE 144 Query: 121 -QHLISPPYVIKPL--KGGSSLGIIVIKKD--QSIPLDLLQSSSWNHGDQLLIEQYVDG- 174 I P ++KP GGS GI +++ + I L S +++LIE+ + G Sbjct: 145 IADEIGYPVIVKPSFGLGGSGGGIAYNEEELEEIIEEGLRASPV----EEVLIEESIIGW 200 Query: 175 IELTCGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFL- 233 E V+ D + + + + + +S V PA+ D ++ R A + Sbjct: 201 KEFEYEVVRDGKDNCI-VVCNMENLD--PMGVHTGDSITVAPAQTLTDKEYQMLRDAAIK 257 Query: 234 AHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMA 278 + IG G F DP +++ +EIN P ++ S A Sbjct: 258 VIREIGIEGGCNIQFAVDPGGGELYVIEIN--PRVSRSSALASKA 300 >gnl|CDD|30788 COG0439, AccC, Biotin carboxylase [Lipid metabolism]. Length = 449 Score = 46.4 bits (110), Expect = 1e-05 Identities = 37/212 (17%), Positives = 83/212 (39%), Gaps = 20/212 (9%) Query: 64 EDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDS--- 120 E+ + + A DK+ ++++++ GVPV P + Sbjct: 87 ENAAFAEACAEAGLTFIGPSAEAIRRMGDKITARRLMAKAGVPVVPGSDGAVADNEEALA 146 Query: 121 -QHLISPPYVIKPLKGGSSLGIIVIKK----DQSIPLDLLQSSSWNHGDQLLIEQYVDG- 174 I P ++K GG G+ V++ + + ++ + ++ +E++++G Sbjct: 147 IAEEIGYPVIVKAAAGGGGRGMRVVRNEEELEAAFEAARGEAEAAFGNPRVYLEKFIEGP 206 Query: 175 --IELTCGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAK-IPLDIYKEVQRLA 231 IE+ V+GD +V + ++ P+ + ++ +++ A Sbjct: 207 RHIEVQ--VLGDGHGNVIHLGE-----RDCSIQRRHQKVIEEAPSPLLTEELREKIGEAA 259 Query: 232 FLAHQAIGCRGISRSDFLFDPLSRKVFWLEIN 263 A + IG RG +FL+D F +E+N Sbjct: 260 VRAAKLIGYRGAGTVEFLYDSNGEFYF-IEMN 290 >gnl|CDD|145768 pfam02786, CPSase_L_D2, Carbamoyl-phosphate synthase L chain, ATP binding domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold. Length = 211 Score = 36.5 bits (85), Expect = 0.008 Identities = 41/184 (22%), Positives = 78/184 (42%), Gaps = 19/184 (10%) Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMD-SQHL---ISPPYVIKPLKGGSSLGIIVIKKD 147 DK+ K + GVP P T + + I P +IK GG LG+ + + + Sbjct: 1 DKVLFKAAMKEAGVPTVPGTAGPVETEEEALAAAKEIGYPVIIKAAFGGGGLGMGIARNE 60 Query: 148 ----QSIPLDLLQSSSWNHGDQLLIEQYVDG---IELTCGVMGDASLDVTEIAVPKSDFY 200 + L L ++ + Q+L+E+ + G IE V+ DA + I V + Sbjct: 61 EELAELFALALAEAPAAFGNPQVLVEKSLKGPKHIEYQ--VLRDAHGNC--ITVCNRECS 116 Query: 201 SYELKYSSLNSTHVLPAK-IPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFW 259 + + S V P++ + + + ++ A + +G G +F DP S + ++ Sbjct: 117 ---DQRRTQKSIEVAPSQTLTDEERQMLREAAVKIARHLGYVGAGTVEFALDPFSGEYYF 173 Query: 260 LEIN 263 +E+N Sbjct: 174 IEMN 177 >gnl|CDD|35459 KOG0238, KOG0238, KOG0238, 3-Methylcrotonyl-CoA carboxylase, biotin-containing subunit/Propionyl-CoA carboxylase, alpha chain/Acetyl-CoA carboxylase, biotin carboxylase subunit [Lipid transport and metabolism, Amino acid transport and metabolism]. Length = 670 Score = 35.7 bits (82), Expect = 0.016 Identities = 40/186 (21%), Positives = 79/186 (42%), Gaps = 24/186 (12%) Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGIIVIK 145 DK SKQ++ + GVP+ P + + I P +IK GG G+ + Sbjct: 111 DKSTSKQIMKAAGVPLVPGY--HGEDQSDEEAKKVAREIGYPVMIKATAGGGGKGMRIAW 168 Query: 146 KDQSIPLDLLQSSSWNHG-----DQLLIEQYVDG---IELTCGVMGDASLDVTEIAVPKS 197 ++ + L+S+ D +L+E+++D IE+ V GD + + + + Sbjct: 169 SEEEF-EEGLESAKQEAAKSFGDDGMLLEKFIDNPRHIEVQ--VFGDKHGNA--VHLGER 223 Query: 198 DFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKV 257 D S + + + P +P + + + A A +A+G G +F+ D Sbjct: 224 DC-SVQRRNQKIIEEAPAPN-LPEETRRALGEAAVRAAKAVGYVGAGTVEFIVDS-KDNF 280 Query: 258 FWLEIN 263 +++E+N Sbjct: 281 YFMEMN 286 >gnl|CDD|145680 pfam02655, ATP-grasp_3, ATP-grasp domain. No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman). Length = 160 Score = 34.3 bits (79), Expect = 0.039 Identities = 31/161 (19%), Positives = 69/161 (42%), Gaps = 24/161 (14%) Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIP 151 DK+++ + + + GVP P L + + Y++KP G G+ ++ + Sbjct: 3 DKLKTYKALKNAGVP-TPETL----SAEEPTEEEKKYIVKPRDGCGGEGVRFVENGREDE 57 Query: 152 LDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIAVPKS--DFYSYELKYSSL 209 + + ++I+++++G L+ ++ D ++V + D Y+ Sbjct: 58 EFI---------ENVIIQEFIEGEPLSVSLLSDGE-KALPLSVNRQLIDNAGSGFVYAG- 106 Query: 210 NSTHVLPAKIPLDIYKEVQRLAFLAHQAI-GCRGISRSDFL 249 N T P++ L +E++ LA +A+ G RG D + Sbjct: 107 NLT---PSRTELK--EELEELAEEVVEALPGLRGYVGVDLV 142 >gnl|CDD|35590 KOG0369, KOG0369, KOG0369, Pyruvate carboxylase [Energy production and conversion]. Length = 1176 Score = 32.3 bits (73), Expect = 0.17 Identities = 38/183 (20%), Positives = 73/183 (39%), Gaps = 18/183 (9%) Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISP----PYVIKPLKGGSSLGIIVIKKD 147 DK+ ++ + GVPV P T++ P +IK GG G+ V++ Sbjct: 147 DKVAARAIAIEAGVPVVPGTPGPITTVEEALEFVKEYGLPVIIKAAYGGGGRGMRVVRSG 206 Query: 148 QSIPLDLLQSSS---WNHGD-QLLIEQYVDG---IELTCGVMGDASLDVTEIAVPKSDFY 200 + + ++ S G+ L +E++++ IE+ ++GD +V + Sbjct: 207 EDVEEAFQRAYSEALAAFGNGTLFVEKFLEKPRHIEVQ--LLGDKHGNVVHLYERDCSVQ 264 Query: 201 SYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWL 260 K + LP ++ I + +LA + +G +FL D R F + Sbjct: 265 RRHQKVVEIAPAKTLPPEVRDAILTDAVKLA----KHVGYENAGTVEFLVDQKGRHYF-I 319 Query: 261 EIN 263 E+N Sbjct: 320 EVN 322 >gnl|CDD|30500 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]. Length = 428 Score = 32.1 bits (73), Expect = 0.17 Identities = 25/111 (22%), Positives = 47/111 (42%), Gaps = 18/111 (16%) Query: 86 ASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLIS------PPYVIKP--LKGGS 137 A+ L K +K + G+P + FT D + + P V+K L G Sbjct: 97 AAQLEGSKAFAKDFMKKYGIP---TAEYEVFT-DPEEAKAYIDEKGAPIVVKADGLAAGK 152 Query: 138 SLGIIVIKKDQ----SIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGD 184 G+IV + ++ L ++ + G +++IE+++DG E + D Sbjct: 153 --GVIVAMTLEEAEAAVDEMLEGNAFGSAGARVVIEEFLDGEEFSLQAFVD 201 >gnl|CDD|110097 pfam01071, GARS_A, Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain. Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02786). Length = 193 Score = 31.5 bits (72), Expect = 0.30 Identities = 22/105 (20%), Positives = 44/105 (41%), Gaps = 18/105 (17%) Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLIS------PPYVIKP--LKGGSSLGIIV 143 K +K + G+P D + S P V+K L G G+IV Sbjct: 2 SKSFAKDFMKRHGIPTAEYETFT----DPEEAKSYIREAGFPAVVKADGLAAGK--GVIV 55 Query: 144 IK-KDQSIPL--DLLQSSSWNH-GDQLLIEQYVDGIELTCGVMGD 184 +++I ++L+ + G+ ++IE++++G E++ D Sbjct: 56 AMDNEEAIKAVDEILEQKKFGEAGEPVVIEEFLEGEEVSVLAFVD 100 >gnl|CDD|31301 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]. Length = 386 Score = 31.3 bits (71), Expect = 0.33 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 6/69 (8%) Query: 22 CASALEDAGFKVSQIDVDR----SVGLVLAHLKPDLA-FNVLHGNFGEDGLVQAILELLE 76 LE GF+V+ + VD + + L+PD +++H N E G +Q I E+ E Sbjct: 107 TCRYLERQGFEVTYLPVDSNGLVDLEQLEEALRPDTILVSIMHAN-NETGTIQPIAEIGE 165 Query: 77 IPYTHSGIL 85 I + Sbjct: 166 ICKERGILF 174 >gnl|CDD|35119 COG5560, UBP12, Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]. Length = 823 Score = 28.4 bits (63), Expect = 2.5 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 3/50 (6%) Query: 51 PDLAFNVLHGNFGEDGLVQAILELLEIPY---THSGILASALSMDKMRSK 97 P L NVL D LV+ ELL + T +++ + + + S Sbjct: 562 PFLQLNVLIKASIYDKLVKEFEELLVLVEMKKTDVDLVSEQVRLLREESS 611 >gnl|CDD|48539 cd02990, UAS_FAF1, UAS family, FAS-associated factor 1 (FAF1) subfamily; FAF1 contains a UAS domain of unknown function N-terminal to a ubiquitin-associated UBX domain. FAF1 also contains ubiquitin-associated UBA and nuclear targeting domains, N-terminal to the UAS domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. It is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kB (NF-kB) by interfering with the nuclear translocation of the p65 subunit. FAF1 also interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway.. Length = 136 Score = 28.4 bits (63), Expect = 2.5 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 4/70 (5%) Query: 10 SEREVSLSSGKACASALEDAGFKVSQIDVDR--SVGLVLAHLKPDLAFNVLHGNFGEDGL 67 S + LSS ++ A + I D+ ++ +++ + NV+ GN G D L Sbjct: 68 SNKARFLSSCTRHFGSV--AAQTIRNIKTDQLPAILIIMGKRSSNEVLNVIQGNTGVDEL 125 Query: 68 VQAILELLEI 77 + ++E +E+ Sbjct: 126 LMRLIEAMEM 135 >gnl|CDD|31240 COG1038, PycA, Pyruvate carboxylase [Energy production and conversion]. Length = 1149 Score = 28.3 bits (63), Expect = 2.7 Identities = 40/189 (21%), Positives = 76/189 (40%), Gaps = 30/189 (15%) Query: 92 DKMRSKQVVSSCGVPVCPSILVNRFTMD----SQHLISPPYVIKPLKGGSSLGIIVIKKD 147 DK++++ GVPV P T++ P +IK GG G+ V++ + Sbjct: 121 DKVKARNAAIKAGVPVIPGTDGPIETIEEALEFAEEYGYPVMIKAAAGGGGRGMRVVRSE 180 Query: 148 QSIPLDLLQSSSWNHG----DQLLIEQYVDG---IELTCGVMGDASLDVTEIAVPKSDFY 200 + ++ S D++ +E+ V+ IE+ ++GD +V + Sbjct: 181 ADLAEAFERAKSEAKAAFGNDEVYVEKLVENPKHIEVQ--ILGDTHGNVVHL-------- 230 Query: 201 SYELKYSSLNSTH-----VLPAK-IPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLS 254 +E + S+ H V PA + ++ E+ A + IG +FL D Sbjct: 231 -FE-RDCSVQRRHQKVVEVAPAPYLSPELRDEICDDAVKLARNIGYINAGTVEFLVDEDG 288 Query: 255 RKVFWLEIN 263 + F +E+N Sbjct: 289 KFYF-IEVN 296 >gnl|CDD|31775 COG1587, HemD, Uroporphyrinogen-III synthase [Coenzyme metabolism]. Length = 248 Score = 28.1 bits (62), Expect = 3.2 Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 4/59 (6%) Query: 19 GKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFN----VLHGNFGEDGLVQAILE 73 G+ A AL G KV I D +L L L +L GN G + L + + E Sbjct: 86 GEKTAEALRKLGIKVDFIPEDGDSEGLLEELPELLKGGKRVLILRGNGGREVLEEKLEE 144 >gnl|CDD|36256 KOG1038, KOG1038, KOG1038, Mitochondrial/chloroplast DNA-directed RNA polymerase RPO41, provides primers for DNA replication-initiation [Transcription, Replication, recombination and repair]. Length = 1088 Score = 27.6 bits (61), Expect = 4.4 Identities = 11/47 (23%), Positives = 22/47 (46%) Query: 211 STHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKV 257 + +++P+ P D+Y V + +G + L D ++RKV Sbjct: 802 AVNLVPSDKPQDVYSAVAARVEKIMKQDAEKGPEVAKILKDQVTRKV 848 >gnl|CDD|30680 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein]. Length = 323 Score = 27.1 bits (60), Expect = 6.3 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 9/48 (18%) Query: 20 KACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAF----NVLHGNFG 63 +A ALEDAG ID +++A PD F ++ G Sbjct: 58 EAARKALEDAGISPDDID-----LIIVATSTPDHLFPSTACLVQARLG 100 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 0.320 0.137 0.401 Gapped Lambda K H 0.267 0.0732 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,588,552 Number of extensions: 185817 Number of successful extensions: 452 Number of sequences better than 10.0: 1 Number of HSP's gapped: 441 Number of HSP's successfully gapped: 19 Length of query: 300 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 207 Effective length of database: 4,254,100 Effective search space: 880598700 Effective search space used: 880598700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 57 (25.7 bits)