Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011384981.1 AMB_RS13085 AMP-binding protein
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000009985.1:WP_011384981.1 Length = 517 Score = 155 bits (391), Expect = 5e-42 Identities = 115/377 (30%), Positives = 187/377 (49%), Gaps = 33/377 (8%) Query: 184 VAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYH 243 VA L+Y+SGTTG PKGVM+ HRNI+ FI +S G GD LP H Sbjct: 165 VAALIYTSGTTGTPKGVMLPHRNIM------FIGA---VSGGLRDIGSGDVAYGVLPMSH 215 Query: 244 IYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVD-- 301 ++GL ++ L+ G L V +F + A ++ ++ VP + +H + Sbjct: 216 VFGLASVLVGTLFGGACLHVAPRFAPAQVLADLKAGLTMWNG-VPAMFAKFLEHIRLTGA 274 Query: 302 KYDLSSLRMMNSGAAPLTQEL---VEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREA 358 K + +LR +++G +PL + EA++ ++ + GYGL+E++PT R + R Sbjct: 275 KVEAPALRFLSAGGSPLDPAIKAETEALFGQV---LNNGYGLTESAPTICQTRLDAPRSD 331 Query: 359 MGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSE 418 SVG +P ++ + + G K++ +G+VGEL+ +GP GY+ P+ T+ + Sbjct: 332 C-SVGHALPGVEVRIV-----GEGGKDMPDGQVGELWSRGPGTMKGYYRAPDMTREVIDA 385 Query: 419 DGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIES 478 +GW TGD +D G +I R KELI GF V PAE+E + + AV+G + Sbjct: 386 EGWLNTGDFARRDPDGALFIVGRAKELIIRSGFNVYPAEVEAVFNAHPLVTHSAVVGRPA 445 Query: 479 ETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNP 538 EV V+ A G++E + +W +++A +KR G V V +P Sbjct: 446 ADGNEEV--VAFVQVAPGTELGSAE------LTEWAAARLAPYKR-PGEVVVVGHLPAGA 496 Query: 539 SGKILRRILKQKFKGAA 555 +GKIL+ L + + A Sbjct: 497 TGKILKNRLAEAARNHA 513 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: 659 Number of extensions: 33 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