Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate CCNA_03292 CCNA_03292 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Caulo:CCNA_03292 Length = 517 Score = 166 bits (420), Expect = 2e-45 Identities = 147/489 (30%), Positives = 234/489 (47%), Gaps = 41/489 (8%) Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129 G+ +A+ +SI + G L AG ++P P T + +A + + AK A V Sbjct: 63 GEAVAVCALSSIPYAALFLGALRAGVAVAPIAPSSTPESIAGMVADCGAKLFFLDAGVA- 121 Query: 130 VAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVY 189 EA K +P I L G + F + AT +I P K ++Y Sbjct: 122 ---EAQKPAPVPVRPIALDGSSAG-----QAFDAWLAPEDATP-TPVEIGP-KHPFNIIY 171 Query: 190 SSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTC 249 SSGTTG PKG++ SH +R + I G+ + + P L P Y L C Sbjct: 172 SSGTTGTPKGIIQSH-----GMRWKHIFVGDAIGYGHTPVS-----LLSTPLYSNTTLVC 221 Query: 250 LITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLR 309 L G +++M KFD+ ++ +R + + +VP L +HP D+YDLSS R Sbjct: 222 FFP-TLAGGGTVVLMKKFDVVRYLELAAKHRITHTMLVPVQYRRLMEHPDFDRYDLSSTR 280 Query: 310 MMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNM 369 M +AP +L V R G+ + +G++E T E + + +VGR P Sbjct: 281 MKFCTSAPFAADLKAQVLKRWPGGLVEYFGMTEGGGTCILMAHEH-PDKLHTVGRPAPGH 339 Query: 370 QAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGC--LSEDGW--FQTG 425 + + EDG ++VG G VGE+ + ++ GYH P+ T +S +GW +TG Sbjct: 340 DIR--LVDEDG---RQVGPGVVGEIVGRSASMMNGYHGRPDKTAEATWVSPEGWTFIRTG 394 Query: 426 DVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEV 485 DVG D +G + DR K++I GF + P++LE LV + A+ + AV+G+ S+ G E Sbjct: 395 DVGRFDEEGFLTLMDRKKDMIISGGFNIYPSDLEAVLVQHPAVFEAAVVGVPSDAWG-ET 453 Query: 486 PMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRR 545 P+A V KSS +E D I +++ +V +RL V VD +P++ GK+L+R Sbjct: 454 PVAFVA----LKSSQVAEAD---AIKTFVNGQVGKTQRL-AEVVVVDSLPRSHIGKVLKR 505 Query: 546 ILKQKFKGA 554 L+ ++ + Sbjct: 506 ELRDSWQNS 514 Lambda K H 0.317 0.136 0.410 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: 661 Number of extensions: 43 Number of successful extensions: 4 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: 562 Length of database: 517 Length adjustment: 35 Effective length of query: 527 Effective length of database: 482 Effective search space: 254014 Effective search space used: 254014 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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