Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_013092306.1 BC1002_RS22570 FAD-binding oxidoreductase
Query= BRENDA::Q8U1G2 (382 letters) >NCBI__GCF_000092885.1:WP_013092306.1 Length = 441 Score = 153 bits (386), Expect = 1e-41 Identities = 119/424 (28%), Positives = 186/424 (43%), Gaps = 61/424 (14%) Query: 2 IPEKSEIVVIGGGIVGVTIAHELAKRGEEVTLVEKRFIGSGSTFRCGTGIRQQFNDEANV 61 +P +++VVIGGGI+GV A+ LA+RG V LVEK IG+ + R RQQ D + Sbjct: 14 LPTAADVVVIGGGIIGVFAAYYLARRGISVALVEKGRIGAEQSSRNWGWCRQQNRDAREL 73 Query: 62 QVMKRSVELWKKYSEEYG--FKFEQTGYLFLLYDDEEVEIFKQNIKIQNKFGVPTRLITP 119 + +S++LW++++ E G F + G L+L DD E+ + GV T ++ Sbjct: 74 PMASKSLDLWERFAAESGEDTGFHRCGLLYLSNDDAELSRWSSWGDFAKTAGVTTCMLDS 133 Query: 120 EEAKEIVPLLDISEVIAASW-----NPTDGKADPFHSTTAFALKAKEYGAKILEYTEVKG 174 +A E + +W +P+DG ADP + A A + G + ++ +G Sbjct: 134 RQAAE------RGQATGRAWKGGVFSPSDGTADPGKAAPAVAAALMKLGGSVHQHCAARG 187 Query: 175 FIIENNEIKGVKTNRGVIKTGIVVNATNAWAKLINAMAGIK--------TSIPIEPYKHQ 226 +E + GV T GVIKT V A AWA GI+ + + + P +H+ Sbjct: 188 LELEGGRVSGVVTEAGVIKTRTAVLAGGAWASSFCRQLGIRFPQASVRQSILSVSPVEHR 247 Query: 227 ---AVITQPIK-----------------RGTIKPMVISFKYGHAYLTQTAHGGII-GGV- 264 A+ T + R + P + F + ++ GG+ Sbjct: 248 LPDALFTAGVSVTRRNDGRYALAISGRARVDVTPQFMRFAPQFVPMFAKRWRNLLPGGLE 307 Query: 265 ----GYEV-------GPT-------YDLTPTYEFLREVSYYFSKIIPALKNLLILRTWAG 306 G+E PT D P ++E +++P L+ I WAG Sbjct: 308 GIRGGHETLRRWRLDAPTPMERVRILDPKPDPAAVKETHRRAVELLPDLREAKITHAWAG 367 Query: 307 YYAKTPDSNPAIGKVEGVSDYYIAAGFSGHGFMMAPAVAEMVADLITKGKTELPVEWYDP 366 + TPD P IG+V G +AAGFSGHGF + P ++ADL T + + Y P Sbjct: 368 FVDSTPDGVPGIGEVPGTPGLILAAGFSGHGFGIGPGAGHLIADLATGAEPIVDPIPYQP 427 Query: 367 HRFE 370 RF+ Sbjct: 428 SRFD 431 Lambda K H 0.318 0.137 0.402 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: 379 Number of extensions: 17 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: 382 Length of database: 441 Length adjustment: 31 Effective length of query: 351 Effective length of database: 410 Effective search space: 143910 Effective search space used: 143910 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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