Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Pf6N2E2_2872 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2872 Length = 563 Score = 193 bits (491), Expect = 1e-53 Identities = 158/522 (30%), Positives = 245/522 (46%), Gaps = 30/522 (5%) Query: 46 LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 +T +L S AA L++ + LQ GDR+ + N L +PV G I AG I NP + Sbjct: 50 ITYGELYELSGAFAAYLQQHTDLQPGDRIAVQLPNVLQYPVAVFGAIRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTS---------IYDG 155 ARE+ +Q DSGA L+C +N L A K H+ + + + + Sbjct: 110 TAREMEHQFNDSGAKALVCLANMAH--LAEAVVPKTSVKHVIVTEVADLLPPLKRLLINS 167 Query: 156 VTNPQKGC--AYWSDLLASEEEGAAFTWDELSTPA--LSSTTLALNYSSGTTGRPKGVEI 211 V K AY + + D+ + A S L Y+ GTTG KG + Sbjct: 168 VIKYVKKMVPAYHLPKAVKFNDVLSKGHDQPVSEANPTSDDVAVLQYTGGTTGVAKGAML 227 Query: 212 SHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAALYRATPVYI 270 +HRN VANMLQ + + + + LP+YH A +A L + I Sbjct: 228 THRNLVANMLQCKALMGSNLNEGCEI----LITPLPLYHIYAFTFHCMAMMLIGNHNILI 283 Query: 271 MSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVC 330 + D M++ +++ + F+ + + VAL + A + D S++++ SG L Sbjct: 284 SNPRDLPAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSALKVTLSGGMALQLAAA 343 Query: 331 EEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGVEVK 390 E + + I +G+GMTE T V NP + ++G + K++ D + Sbjct: 344 ERWKAVTG---CPICEGYGMTE-TSPVATVNPIQNIQIGTIGIPVPSTLCKVINDAGVEQ 399 Query: 391 ERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELI 450 GEL V+ P VMKGYW+ + AT E +GWL TGDIA + DG +VDR K++I Sbjct: 400 PLGEIGELCVKGPQVMKGYWQRQDATDEILDSEGWLKTGDIALIQPDGYMRIVDRKKDMI 459 Query: 451 KVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIAHYL 509 + G V P ELE +L P + A IG+ + E + ++V RPG + T ++ ++ Sbjct: 460 LISGFNVYPNELEDVLATLPGVLQCAAIGIPDEKSGEAIKIFIVARPGVTLTKEQVMEHM 519 Query: 510 DNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEELR 551 V+ +K + V F +A+P GKILR +LR+ EELR Sbjct: 520 RANVTGYK-VPKAVEFRDALPTTNVGKILRRELRD---EELR 557 Lambda K H 0.319 0.134 0.403 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: 663 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 563 Length adjustment: 36 Effective length of query: 520 Effective length of database: 527 Effective search space: 274040 Effective search space used: 274040 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: 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