Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate H281DRAFT_00360 H281DRAFT_00360 hypothetical protein
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Burk376:H281DRAFT_00360 Length = 402 Score = 427 bits (1099), Expect = e-124 Identities = 212/404 (52%), Positives = 281/404 (69%), Gaps = 10/404 (2%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MDLNF+ EE AFR+EV F +D +P K+ GR T+++M W+ ILN++GW HW Sbjct: 1 MDLNFTPEEEAFREEVLAFLRDKLPQHLADKVHGGRRLTRDDMAGWHAILNERGWLANHW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P EYGG GW++VQ +IF E A AP+ + FGV+M+GPV+ +GSE QK+ +LPRI + Sbjct: 61 PAEYGGPGWTAVQKFIFENECALAGAPRIVPFGVNMLGPVLIRYGSESQKRHWLPRILDG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKA----EKKGDKWIINGQKTWTTLAQHADWIFCLCRTD 176 DWWCQG+SEPG+GSDLAS+KT A + G+ +I+NGQKTWTTL +A+ IFCL RT Sbjct: 121 SDWWCQGYSEPGAGSDLASVKTTAVRGVDADGEHYIVNGQKTWTTLGHYANMIFCLVRTA 180 Query: 177 PAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDY 236 +KQEGISF+L+DMKT G+ VRPI T+DG HEVNEVFF DV VP ENLVG+ENKGW Y Sbjct: 181 TDVRKQEGISFLLIDMKTPGVEVRPIITLDGEHEVNEVFFTDVRVPAENLVGEENKGWTY 240 Query: 237 AKFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALE 296 AK+LL ERT IA VG S + R++++AA+ + G+P+ EDP F ++A VEI+L+ ++ Sbjct: 241 AKYLLTYERTNIAGVGFSVAAVNRLRKIAAKQQRNGRPLCEDPAFAARMARVEIDLENMK 300 Query: 297 LTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSN 356 T LRV+A G G P SS+LKI+G+EI+Q + L +GP+A P+ D Sbjct: 301 TTNLRVIA--AVAGGGVPGAESSMLKIRGTEIRQEISSLTRRAMGPYAQPFIEEALHDGY 358 Query: 357 ETM----DWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 + + A A YFNNRK+SI+GGSNEIQ+NII K +LGL Sbjct: 359 QGAPVGPEEAASAASLYFNNRKLSIFGGSNEIQKNIISKMILGL 402 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: 503 Number of extensions: 14 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: 396 Length of database: 402 Length adjustment: 31 Effective length of query: 365 Effective length of database: 371 Effective search space: 135415 Effective search space used: 135415 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