Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3746 PGA1_262p01500 sarcosine oxidase subunit alpha
Query= BRENDA::Q76M76 (483 letters) >FitnessBrowser__Phaeo:GFF3746 Length = 988 Score = 122 bits (307), Expect = 4e-32 Identities = 130/522 (24%), Positives = 213/522 (40%), Gaps = 111/522 (21%) Query: 19 VTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKVNG-- 76 ++ F+G+ E ++G+T+A AL A G++++ S + HRPRG+ A + + LV++ Sbjct: 22 LSFQFDGKTYEGHQGDTLASALLANGVQLMGRSFKYHRPRGVLTAGSEEPNALVELRSGG 81 Query: 77 --VPNVRSCITLVEEGMKVEMQR------------------------------------- 97 PN R+ + + G++ Q Sbjct: 82 RQEPNTRATVVELFAGLEARSQNRWPSLDHDMMAINDRFSNFLTAGFYYKTFMWPKAFWE 141 Query: 98 -----------GKETLPKGAKPPAWKDAPRYKADVVVIGGGPAGLMAAIHAADAGASVIL 146 G +L A P A+ D D+++IG GP GL AA+ A AGA VIL Sbjct: 142 KLYEPIIRKAAGLGSLTGEADPDAY-DKGYLHCDLLIIGAGPTGLAAALTAGRAGAQVIL 200 Query: 147 IDENPMLGGQLVKQTHKFFGKREQFAGVRGVKIAEILGEEVKKRGNIEVFLETSAVGVFH 206 +E+ LGG+L+ +T + +G V + E+ N+ V T+ G + Sbjct: 201 AEEDYRLGGRLLSETKAL----SEMSGTDWVAQTQA---ELAALPNVRVMPRTTVFGAYD 253 Query: 207 EGEEKLVAAVRKNKE-------------LLEFLGKTLVVATGAMEKMIPFENNDLPGIYG 253 G + AV +N + L K ++ATGA+E+ I FENND PG+ Sbjct: 254 HG---IYGAVERNADHVPTPTAGKPRQTLWRIYSKRALIATGAIERPIAFENNDRPGVML 310 Query: 254 AGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEAMPKVGGYFVHAA 313 AGA + N + PG V+I G+ A L+ GVEV AIV+ V Sbjct: 311 AGAARAYANRWAATPGQSVVIFANGDDAYHTARDLMAKGVEVPAIVD---------VRDG 361 Query: 314 KVRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPS 373 G +L I+ +G+ + + R G + D +A++ G P+ Sbjct: 362 APTLPGTEVLAGAEIIDTKGRLGLSSVTV-------RLANGQTRTIACDALAVSGGWNPN 414 Query: 374 IEL-LHQAGCQV--KFVRELSGHVAVRDGRM--------ETTVQGIFVAGDSAGIEEATT 422 + L HQ G V ++ + G++ TT Q + G E A Sbjct: 415 LGLTCHQRGRPVWSDAIQSFVPGTGLPAGQLVAGAAMGGMTTAQAL-----KGGAERAVE 469 Query: 423 AMLEGKIAGIAAALKAGAASPEWLA---EIEKAQRDLLEFRS 461 A+ + I+ AA L +P L ++ A+R L+F++ Sbjct: 470 ALGDLGISARAADLPQAEDAPVSLTPFWHVKGAKRAWLDFQN 511 Lambda K H 0.319 0.138 0.397 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: 1019 Number of extensions: 42 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 483 Length of database: 988 Length adjustment: 39 Effective length of query: 444 Effective length of database: 949 Effective search space: 421356 Effective search space used: 421356 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 (21.8 bits) S2: 54 (25.4 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