Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF1301 Psest_1334 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__psRCH2:GFF1301 Length = 562 Score = 231 bits (590), Expect = 5e-65 Identities = 159/514 (30%), Positives = 254/514 (49%), Gaps = 52/514 (10%) Query: 78 LTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMAR 137 L PGDR+ I N ++ + + GL++VN NP Y + E+ + G + LV + Sbjct: 72 LQPGDRIAIQMPNLLQYPIAVFGALRAGLIVVNTNPLYTSREMRHQFQDSGARALVYLNT 131 Query: 138 FKTSDYLGMLRELAPEWQGQQPGHLQAAK-LPQLKTVV----------WIDDEAGQGADE 186 F + ++E+ P+ + ++ LP LK V+ + D + Sbjct: 132 FGHN-----VQEVLPDTAIEHLIEVRIGDMLPPLKGVLVNAAVKHLKKMVPDYS-----L 181 Query: 187 PGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGF 246 P + F +++ G R A L+ +Q+T GTTG KGA LTH N++ N Sbjct: 182 PQAISFKDVLRDG----ARHNHKPAPLELDHVAVLQYTGGTTGVAKGAMLTHGNLVANMQ 237 Query: 247 FIGECMKLTPA----------DRLCIPVPLYHCFGMVLGNLACFT----HGATIVYPND- 291 + M+ + + P+PLYH + + N C H I P D Sbjct: 238 QVRANMQQLDEHGHPIIREGQEVMIAPLPLYHIYAFTV-NCMCMVVTGNHNVLITNPRDI 296 Query: 292 -GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMK 350 GF ++ +Q + + G+ T+F+A + HP+F + + S L+ G+ + V + Sbjct: 297 NGF-----VKELQRWQFSAFLGLNTLFVALMAHPQFKKIDFSRLKGTNSGGTALVSAVAE 351 Query: 351 RVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVV 410 R + M + YG+TETSPV C + R+ TVG P VK++D D G + Sbjct: 352 RW-KSMTGCTVVEGYGLTETSPVVCANPHGE--HSRLGTVGLPVPGTTVKVID-DEGNAL 407 Query: 411 PIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMV 470 P+G+RGE C KG VM GYW T E +DE GW+ TGD+A +D +G+V+IV R KD++ Sbjct: 408 PLGERGELCVKGPQVMKGYWQRPDATAEVLDEEGWLKTGDIAVIDEDGFVSIVDRKKDLI 467 Query: 471 IRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFC 530 I G N+YP EIE+ + HP+V +GV D+K GE + +++ T +D++ A+C Sbjct: 468 IVSGFNVYPNEIEDVVMAHPKVAACAAIGVADEKSGEAVKLFVVPSDPTL-DQDELHAYC 526 Query: 531 KGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 + YK+PR+ F + PMT GKI + ++RD Sbjct: 527 RENFTGYKMPRHYVFRDALPMTPVGKILRRELRD 560 Lambda K H 0.320 0.136 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: 786 Number of extensions: 39 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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: 53 (25.0 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