Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate PfGW456L13_2536 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2536 Length = 388 Score = 237 bits (604), Expect = 5e-67 Identities = 150/408 (36%), Positives = 223/408 (54%), Gaps = 35/408 (8%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVE---WYRILNKKGWAV 57 MDL ++ + AFR + R + NVP++ Q +T++ E W LN+ W + Sbjct: 1 MDLTYTPAQQAFRFDARTWLAANVPSEPLQSF-----DTEQGFAEHRAWEAKLNEGRWGM 55 Query: 58 THWPKEYGGTGWSSVQHYIFNEELQAAPAPQPL-AFGVSMVGPVIYTFGSEEQKKRFLPR 116 WP E GG G ++ IF EE + AP + G+ ++GP + +GSEEQK RFLPR Sbjct: 56 VTWPTELGGRGCDLIEWLIFEEEYYRSGAPARVNQNGIFLLGPTLMEYGSEEQKARFLPR 115 Query: 117 IANVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTD 176 +A +D W Q +SEPG+GSD+A++++KAE+ GD ++INGQKTW+T A ADW F + RTD Sbjct: 116 MATGEDIWAQAWSEPGAGSDMAAIRSKAERVGDHYVINGQKTWSTRAVWADWAFGIFRTD 175 Query: 177 PAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDY 236 P +++ G++FIL+ + T GITVRPI ++G E+FFDDV+VP+EN +G E GW Sbjct: 176 PQSQRHHGLTFILLPLNTPGITVRPIPQLNGLPGFAEIFFDDVKVPVENALGGEGMGWHV 235 Query: 237 AKFLLGNERTGIAR-VGMSKERIRRIKQ--LAAQVESGGKPVIEDPKFRDKLAAVEIELK 293 A G ER + R +E +R+ Q LA + ++ P I + R L A E Sbjct: 236 AMSTAGFERGLLLRSPARFQETAKRLVQLYLANREQADRDPAIGEAVMRAWLDA-EAYTL 294 Query: 294 ALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGD- 352 +T ++V GK P SS KI SE+ Q + M ++G + G+ Sbjct: 295 GTYMTASQLVQG------GKIGPESSTNKIFWSELDQRMHDTAMSILG-------LRGEL 341 Query: 353 ----DDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 + + W G+ + IY G+NEIQRNII + +LG+ Sbjct: 342 LPQAPAAGDVGHW----LEGFLFAQAGPIYAGTNEIQRNIIAERMLGM 385 Lambda K H 0.317 0.135 0.411 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: 434 Number of extensions: 22 Number of successful extensions: 5 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: 396 Length of database: 388 Length adjustment: 31 Effective length of query: 365 Effective length of database: 357 Effective search space: 130305 Effective search space used: 130305 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 (21.6 bits) S2: 50 (23.9 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