Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_090443440.1 BLS63_RS09790 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_900100495.1:WP_090443440.1 Length = 562 Score = 190 bits (483), Expect = 1e-52 Identities = 159/527 (30%), Positives = 243/527 (46%), Gaps = 45/527 (8%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 TY L S F L+ + + GD +A+ PN + PVV++G + AG + NP YT Sbjct: 51 TYGELYTLSGQFAAYLQQHTDLQPGDRIAVQLPNVLQYPVVVFGAMRAGLVVVNTNPLYT 110 Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-------- 157 E+ Q +S AK LV A++ +A + K G+ + +GD P R Sbjct: 111 AREMEHQFNDSGAKALVCLANMAHLAEQVVPKTGVKTVIVTEVGDMLPPLKRLLVNSVVK 170 Query: 158 -VKHFTSVRNISGATRY-------RKQKITPAK----DVAFLVYSSGTTGVPKGVMISHR 205 VK + A ++ R Q + A ++A L Y+ GTTGV KG M++HR Sbjct: 171 YVKKMVPAYQLPHAVKFTQALAKGRGQALREANPGSGEIAVLQYTGGTTGVAKGAMLTHR 230 Query: 206 NIVANIRQQFIAEGEMLS-WNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYH-LIV 263 N+VAN+ Q A M S N G + ++A LP YHIY T + G H +++ Sbjct: 231 NLVANMLQ---ARAMMASNMNEG----SEVIVAPLPLYHIYAFTFHCMAMMLIGSHNVLI 283 Query: 264 MSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELV 323 + D+ + + Y+ S + + + L + K D SSL++ SG L Sbjct: 284 TNPRDLPGMVSDLAKYKFSGFVGLNTLFVALCNNADFQKLDFSSLKVTLSGGMALQLATA 343 Query: 324 EAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEP 383 E I +G+G++ETSP ++ + +G++G +P+ K + +D Sbjct: 344 ERWKQVTGSPICEGFGMTETSPVASVNPIQNIQ--LGTIGIPVPSTLCKVV---DDAGN- 397 Query: 384 KEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVK 443 E+ G VGEL +KGP V GY + +AT L DGW +TGD+ G I DR K Sbjct: 398 -ELPLGAVGELCVKGPQVMKGYWQRQDATDEILDADGWLKTGDIAVIQDDGYMRIVDRKK 456 Query: 444 ELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSE 503 ++I GF V P ELE L + A IG+ E G + + V AK S T E Sbjct: 457 DMILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFVV---AKPGESLTKE 513 Query: 504 KDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQK 550 +++ + + V +K + V F D +P GKILRR L+ + Sbjct: 514 -----QVMAHMRANVTGYK-VPKAVEFRDALPTTNVGKILRRELRDE 554 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: 31 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: 562 Length adjustment: 36 Effective length of query: 526 Effective length of database: 526 Effective search space: 276676 Effective search space used: 276676 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 24 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