Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF4309 PS417_22070 long-chain fatty acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__WCS417:GFF4309 Length = 562 Score = 135 bits (340), Expect = 4e-36 Identities = 114/377 (30%), Positives = 174/377 (46%), Gaps = 42/377 (11%) Query: 185 DPMILNYTSGTTSSPKGVVHCH----------RGIFIMTVDS---LIDWGVPKQPVYLWT 231 D +L YT GTT KG + H R T D LI G Q V + Sbjct: 208 DIAVLQYTGGTTGLAKGAMLTHGNLVANMQQVRACMSQTGDDGHPLIKEG---QEVMIAP 264 Query: 232 LPMFHANGWSYPWGMAAVGGTNICLRKFDSEI--IYDMIKRHGVTHMCGAPVVLNMLSNA 289 LP++H ++ V G + L +I +K+ T + G + L + Sbjct: 265 LPLYHIYAFTANCMCMMVSGNHNVLITNPRDIGGFIKELKKWRFTGLLGLNTLFVALMDH 324 Query: 290 PGSEPLKTTVQIMT--AGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWN 346 P + L + +T G A R + + G A+ GYGLTET+ + Sbjct: 325 PDFKSLDFSHLKLTNSGGTALIKATAERWQQITGCAIGEGYGLTETSPVA---------- 374 Query: 347 HLPATERARLKSRQG-VGT-VMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLK 404 +T KSR G VG V T + V+D V+ GE+ ++G VM GY + Sbjct: 375 ---STNPYGNKSRLGTVGIPVPATAMKVIDD---HGVELPLGERGELCIKGPQVMKGYWQ 428 Query: 405 DPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPD 464 PE TA+++ A+GW TGD+ V+ +G++ I DR KD+II G N+ E+E ++ +HP Sbjct: 429 QPEATAEALDAEGWLKTGDIAVIDEEGFVSIVDRKKDLIIVSGFNVYPNEIEDVVMAHPA 488 Query: 465 ILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEEL 524 + AV+ PDE GE FV + + + +E+ YC++ Y VPK +V ++ L Sbjct: 489 VANCAVIGVPDERTGEAVKLFVVAR---AEGVSLEELKAYCKTNFTGYKVPKHIVLRDSL 545 Query: 525 PKTSTGKVQKFILRDMA 541 P T GK+ + LRD+A Sbjct: 546 PMTPVGKILRRELRDIA 562 Lambda K H 0.319 0.135 0.412 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: 756 Number of extensions: 44 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: 562 Length adjustment: 36 Effective length of query: 520 Effective length of database: 526 Effective search space: 273520 Effective search space used: 273520 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