Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 3607591 Dshi_1000 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Dino:3607591 Length = 573 Score = 159 bits (401), Expect = 4e-43 Identities = 152/517 (29%), Positives = 224/517 (43%), Gaps = 43/517 (8%) Query: 55 SQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQL 113 S A LR+ +GL GDRV L N L FPV GV AG + NP + A E+ Q Sbjct: 66 SDAFAVYLREVAGLNPGDRVALQMPNCLSFPVAAFGVFKAGCVLVNVNPLYTAEEMGKQF 125 Query: 114 QDSGATYLLCASNSLETGLEAAKQAKLPQ---SHIFAYDTSIYDGVTNPQKGCAYWSDLL 170 D+ L+ + EA + +P + I + ++ G+ + YW + Sbjct: 126 LDAEPHALVIVDMFADKIPEATRGHPIPNIVVTRIAEFLPALPRGIVGLVQ--KYWDRSV 183 Query: 171 A-----------SEEEGAAFTWDE------LSTPALSSTTLALNYSSGTTGRPKGVEISH 213 A + E G DE L Y+ GTTG KG ++H Sbjct: 184 AEIEVPHIRLPDALEAGRRHQADERIEVEGYHQAVAPDDVAVLQYTGGTTGVAKGAMLTH 243 Query: 214 RNYVANMLQYCHTASLHPDYKARLERSR--WLCFLPMYHAMAQNIFIAAALYR-ATPVYI 270 N + NM Q LER R L LP+YH A ++ + + A + I Sbjct: 244 ANLIVNMEQTMELIE-------GLERGREVVLTALPLYHIFAFSLNMLGFYWMGARNILI 296 Query: 271 MSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVC 330 S + + +RIT V + L ++ +G L V Sbjct: 297 PSPRPLANLKRAFENYRITWMSGVNTLFNGLTNEIWFTDTPPRHLKFAAAGGMALQSSVA 356 Query: 331 EEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVG-ELNANCEAKIMFDGVEV 389 E ++ ++ QG+G+TE T + P + S S+G L A A + DG +V Sbjct: 357 ERWREI---TGTDVLQGYGLTE-TSPILSLEPLGKTRSGSIGIPLPATRLACLDDDGKQV 412 Query: 390 KERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKEL 449 RGE+ + P VMKGYW + T ++GW LTGDI +D DG FH+VDR K++ Sbjct: 413 -AIGDRGEIAAKGPQVMKGYWNKPEETANV-LQNGWFLTGDIGVMDADGYFHIVDRKKDM 470 Query: 450 IKVKGNQVAPAELEALLLEHPAISDVAVIGVVIN-NDERPRAYVVLRPGQSATANEIAHY 508 + V G V P E+E L HP I + AVIGV E +A+VV + A+ AH Sbjct: 471 VVVSGFNVYPNEVEDCLASHPGIIEAAVIGVPDGATGEAVKAFVVKGDSGLSEADIRAHC 530 Query: 509 LDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQ 545 ++ ++A+K + V F + +PK+ GKILR LR + Sbjct: 531 KEH-LTAYK-VPKRVEFRDELPKSNVGKILRKDLRAE 565 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: 712 Number of extensions: 45 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 556 Length of database: 573 Length adjustment: 36 Effective length of query: 520 Effective length of database: 537 Effective search space: 279240 Effective search space used: 279240 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