Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4155 Psest_4228 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__psRCH2:GFF4155 Length = 541 Score = 228 bits (581), Expect = 5e-64 Identities = 165/519 (31%), Positives = 250/519 (48%), Gaps = 36/519 (6%) Query: 58 TYAQLQTEAHRLASAL-LGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYR 116 TYA+L + A A L GL PGDR+ + N ++ + + GLV+VN NP Y Sbjct: 46 TYAELGSRADAFARYLRYHAGLQPGDRLALQLPNCLQYPIAVFGALKAGLVIVNTNPQYT 105 Query: 117 TAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWI 176 AE + + G K ++ + R L P+ + +QA + + + Sbjct: 106 AAEARHQFHDSGAKAILVLDR------------LLPQVRA-----VQADTALRQIILTSV 148 Query: 177 DD--EAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGA 234 DD + + E G LRF + + G P Q AGL +Q+T GTTG KGA Sbjct: 149 DDLQQPIYESQEDGTLRFMQALRLGEQRSP--VQREAGLDRL--ALLQYTGGTTGVSKGA 204 Query: 235 TLTHRNILNNGFFIGECMK----LTPADRLCI-PVPLYHCFGMVLGNLACFTHGATIVYP 289 LTHRN+L N E L P + I P+PLYH L+ G V+ Sbjct: 205 MLTHRNLLANVLQTIELFDQPGLLEPEKDVRIAPLPLYHIMAFATNCLSSVGMGLHTVFI 264 Query: 290 NDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVM 349 DG + + +Q + L G+ T+F+ ++HP F + S L+ G+P +EV Sbjct: 265 RDGRNLDETIGAMQRHPFSLLSGINTLFVGLMNHPEFRSIDFSHLKWATSGGAPLNSEVG 324 Query: 350 KRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK-RVSTVGQVQPHLEVKIVDPDTGA 408 +R + + I +G+TE SPV +T T LS R +GQ E++ VD D G Sbjct: 325 RRW-QALTGAPIREGFGLTEASPVV---ATGTQLSPYREGYIGQALIETELRTVD-DEGN 379 Query: 409 VVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKD 468 VP GE +G VM GYW +T + + GW+ TGD+A +D +G+V IV R KD Sbjct: 380 DVPPETPGELWLRGPQVMQGYWQRPDETAKVLTPDGWLKTGDIALLDVDGFVKIVDRKKD 439 Query: 469 MVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRA 528 M++ G N++P EIE+ L +HP V++ VGVPD + GE + ++ K T E + Sbjct: 440 MILVSGFNVFPNEIEDVLMQHPSVRECVAVGVPDARKGEAVKVFVSLKDDT-VDERALLE 498 Query: 529 FCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 C+ + YK+P ++ P T GK+ + ++RDE + Sbjct: 499 HCRQYLTGYKMPSFLELRDELPKTAVGKLLRRQLRDEAR 537 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: 691 Number of extensions: 38 Number of successful extensions: 5 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: 578 Length of database: 541 Length adjustment: 36 Effective length of query: 542 Effective length of database: 505 Effective search space: 273710 Effective search space used: 273710 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