Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 6937793 Sama_1934 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__SB2B:6937793 Length = 558 Score = 214 bits (546), Expect = 5e-60 Identities = 177/568 (31%), Positives = 264/568 (46%), Gaps = 54/568 (9%) Query: 11 DIP-EVDLWTF-----LFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKAL 64 D+P E+D F +FE+ R Y D TY+ L + S F L+ Sbjct: 12 DVPAEIDAGRFDSLVDMFEQAVRDYADQPAFINMGAV---LTYRKLEERSRAFAAYLQNE 68 Query: 65 YEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQ 124 +KGD +AL PN + P+ ++G L AG + NP YT EL QL +S AK +V Sbjct: 69 LGLKKGDRVALMMPNLLQYPIALFGVLRAGLVVVNVNPLYTPRELKHQLIDSGAKTIVVV 128 Query: 125 ASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR------------------VKHFTSVRN 166 ++ E + I +GD R + H S R+ Sbjct: 129 SNFARTLEEVVDDTPVESVIITGLGDLLSAPKRTLVNFVVKYIKKLVPKYDLPHAISFRS 188 Query: 167 ISGATRYRKQKITPAKDV---AFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLS 223 R R Q + P D+ AFL Y+ GTTGV KG M+SH N+VAN+ Q A +L+ Sbjct: 189 ALQKGR-RMQYVKPELDIDTLAFLQYTGGTTGVSKGAMLSHGNVVANVLQANGAYAPLLA 247 Query: 224 WNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKG-YHLIVMSKFDIEKWCAHVQNYRCS 282 DGK + V+ LP YHI+ LT L+KG +L++ + DI + + ++ Y + Sbjct: 248 -----DGK-EFVVTALPLYHIFALTVNCLLFLHKGAQNLLITNPRDIPAFISDLRKYPFT 301 Query: 283 FSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSE 342 V + L + + D S L++ G + + + + S K + +GYGL+E Sbjct: 302 ALTGVNTLFNALVNNEEFTQLDFSRLKLSIGGGMAVQRAVADKWQSITKTRLLEGYGLTE 361 Query: 343 TSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVF 402 SP + + GS+G P +DG+ + +GE GEL+ KGP V Sbjct: 362 ASPLVACCPY-NLEGYNGSIG--FPAPSTLMQVRDDDGNV---LPQGETGELFAKGPQVM 415 Query: 403 LGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYL 462 GY + PE T + +GW TGD+GY D +G FYI DR K++I GF V P E+E + Sbjct: 416 KGYWQRPEETTKVIDANGWLATGDIGYMDEQGFFYIVDRKKDMILVSGFNVFPNEVEDVV 475 Query: 463 VDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHK 522 + + +VA IG+ ++ G V + V AK KS S+ +IK + +K Sbjct: 476 AMHPKVIEVAAIGVPNDASGEIVKVFVV---AKDKSLTESD------VIKHCKHHLTGYK 526 Query: 523 RLRGGVHFVDEIPKNPSGKILRRILKQK 550 + V F DE+PK GKILRR L+ + Sbjct: 527 -VPKLVEFRDELPKTNVGKILRRELRNE 553 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: 686 Number of extensions: 33 Number of successful extensions: 6 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: 558 Length adjustment: 36 Effective length of query: 526 Effective length of database: 522 Effective search space: 274572 Effective search space used: 274572 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: 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