Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate BPHYT_RS22650 BPHYT_RS22650 pyridine nucleotide-disulfide oxidoreductase
Query= BRENDA::Q76M76 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS22650 Length = 428 Score = 132 bits (333), Expect = 2e-35 Identities = 108/342 (31%), Positives = 166/342 (48%), Gaps = 62/342 (18%) Query: 120 DVVVIGGGPAGLMAAIHAADAGASVILIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKI 179 D+V++G GPAGL AA AA AGA+V L+D+NP GGQ+ +Q Sbjct: 6 DIVIVGAGPAGLNAASAAARAGATVALVDDNPRAGGQIWRQ------------------- 46 Query: 180 AEILGEEVKKRGNIEVFLETSAVG----VFHEGEEKLVAAVRKNKELL---EFLG----- 227 G + + FL +A+G + H ++VA + + LL EF G Sbjct: 47 ----GPGHAPQAQLRSFL--TAIGEQNAITHWPSTRVVAPLSRRGLLLESTEFGGACVTY 100 Query: 228 KTLVVATGAMEKMIPFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQ 287 + L++ATGA E+++PF LPG+ GAGA+Q L+ G+R++I G+G + + Sbjct: 101 ERLILATGARERLLPFAGWTLPGVTGAGALQALIKGGMPVRGERIVIAGSGPLLIAALAT 160 Query: 288 LIQAGVEVKAIVEA-----MPKVGGYFVHA-AKVRR--------LGVPILTRHTILRAEG 333 AG V A+VE + + G + A AK+R+ G+ T + A+G Sbjct: 161 ARAAGARVAAVVEQASAFYVARFGVSLLAAPAKLRQAVGMTRGFAGLRYWTGSVVEEAQG 220 Query: 334 KDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPSIELLHQAGCQVKFVRELSGH 393 + RVER + E G + D +A GL P+I L GC + E+ Sbjct: 221 EGRVERVTVRCGRE------GRRVTLDCDRVACGYGLVPNITLAQALGCAIGEAGEI--- 271 Query: 394 VAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGKIAGIAAA 435 V DG+ T+V+ +F AG+ G+ A A +EG+IAG+AA+ Sbjct: 272 --VVDGKQRTSVESVFAAGECTGVGGAELAGVEGEIAGLAAS 311 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: 495 Number of extensions: 32 Number of successful extensions: 7 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: 483 Length of database: 428 Length adjustment: 33 Effective length of query: 450 Effective length of database: 395 Effective search space: 177750 Effective search space used: 177750 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: 51 (24.3 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