Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 3608151 Dshi_1556 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Dino:3608151 Length = 519 Score = 187 bits (476), Expect = 6e-52 Identities = 155/519 (29%), Positives = 230/519 (44%), Gaps = 37/519 (7%) Query: 14 PAIKIPERYNAADDLIGRNLLAGRGGKT---VYIDDAGSYTYDELALRVNRCGSALRTTL 70 PA P +N A G L AG K V A +T+ +L V +ALRT Sbjct: 25 PAAPCPAPFNLA----GYVLAAGDEDKIALEVLGGGAVRWTFGDLRRAVAGYAAALRTE- 79 Query: 71 GLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ 130 GL P D++L+ + + ++FP FL A+ GVVP+ + LT + +++ D A + V + Sbjct: 80 GLAPGDKLLMRLGNTVEFPLLFLAAVAAGVVPVPTSAALTVEEVDWIAADLAPALTVQAP 139 Query: 131 ELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGS 190 + P G+V LE AL+ P PD + +Y+SGS Sbjct: 140 GVA---GPSRGRVVALE--------------ALVPDRDAPLAPVPGDPDRMAYVVYTSGS 182 Query: 191 TGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATA 250 +G P+ H H I + R G+ D + A + Y LG GL+ P A+GATA Sbjct: 183 SGRPRAVAHAHR-AIWARRMMWRDWYGMGPEDRILHAGAFNWTYTLGVGLLDPWAMGATA 241 Query: 251 VLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPE 310 ++ AA+ E L IF VP +Y +L P+ RLR +AGEALP+ Sbjct: 242 LIPEAGTDSAALPEALAASGASIFAAVPGVYRQILKQEALPRLP--RLRHGLTAGEALPD 299 Query: 311 DVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEIT 370 + W+ R G ++ + +G +E ++ G +G G R+ +D DG E+ Sbjct: 300 SLRAAWRDRVGTELYEALGMSECSTFISAHPGRQAPPGHAGFAQAGRRIAALDADGVEVA 359 Query: 371 --TAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDM 428 T+GV G + G ++ + + G+W +GD + +G Y GR DDM Sbjct: 360 RGTSGVLGVHR--GDPGLMLGYLEGGRPRLPLTGDWFVTGDMVEIASDGAVRYLGRGDDM 417 Query: 429 LKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDL 488 + G VSP+EVE A + EAA V + IK ++ A L Sbjct: 418 MNAGGFRVSPLEVEKAFHGRPEIGEAAAV-----EVKIKADVTVIALFYVAAAPVTEAAL 472 Query: 489 KAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRSA 527 A LA YK PR V+ LPK TGK+ R LR+A Sbjct: 473 AAEAAQHLARYKQPRLYIPVETLPKGRTGKLDRRALRAA 511 Lambda K H 0.319 0.138 0.412 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 783 Number of extensions: 46 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 527 Length of database: 519 Length adjustment: 35 Effective length of query: 492 Effective length of database: 484 Effective search space: 238128 Effective search space used: 238128 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory