Align aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) (characterized)
to candidate 8501222 DvMF_1956 Aldehyde ferredoxin oxidoreductase (RefSeq)
Query= BRENDA::Q51739 (605 letters) >FitnessBrowser__Miya:8501222 Length = 575 Score = 285 bits (728), Expect = 5e-81 Identities = 206/575 (35%), Positives = 292/575 (50%), Gaps = 41/575 (7%) Query: 7 RFIRVNLSTGDIKVEEYDEELAKKWLGSRGLAIYLLLKEMDPTVDPLSPENKLIIAAGPL 66 +FIR+++ + ++ E+ A L RGL + E+ PT PL NKL+ A G L Sbjct: 3 KFIRIDMGSRTAEIGACPEKYAG--LAGRGLTSMFIADEVKPTCHPLGKYNKLVFAPGFL 60 Query: 67 TGTSAPTGGRYNVVTKSPLTGFITMANSGGYFGAELKFAGYDAIVVEGKAEKPVYIYIK- 125 TGTSA GR + KSPLTG I +NSGG F ++ A+V EG Y +K Sbjct: 61 TGTSAVNSGRISCGAKSPLTGGIKESNSGGSFSQKMARLDIKALVFEGLPADGKYAVVKV 120 Query: 126 -DEHIEIRDA-SHIWGKKVSETEATIRKEVGSEKVKIASIGPAGENLVKFAAIM----ND 179 + + +A + I G + ++ + G KV +A IGPAGE + A I Sbjct: 121 DKDGVTFDEAPAEIMGAGNYDAIRVLQDKYG-PKVGVALIGPAGEMKLTAANISFADPEG 179 Query: 180 GHRAAGRGGVGAVMGSKNLKAIAVE--GSKTVPIADKQKFMLVVREKVNKLRNDPVAGGG 237 R+AGRGG+GAVMGSK +KA+ ++ G+ VPIA ++F + N L PV G G Sbjct: 180 NIRSAGRGGLGAVMGSKGIKAVVIDDAGAPAVPIAKPEEFKSAAKRFANALTTHPVTGQG 239 Query: 238 LPKYGTAVLVNIINENGLYPVKNFQTGVYPYAYEQSGEAMAAKYLVR-NKPCYACPIGC- 295 LPKYGT VLVNI+NE G P +NF+ G +A GE MAA R K + C GC Sbjct: 240 LPKYGTNVLVNILNEAGGLPTENFRRGRNEWANNIGGETMAATIEERGGKTTHGCHAGCV 299 Query: 296 --GRVNRLPTVGE--TEGPEYESVWALGANLGINDLASIIEANHMCDELGLDTISTGGTL 351 + + G+ T G EYE++WALGA+ I+DL +I A+ DE+G+D+I T + Sbjct: 300 IRCSQHYVDKQGKYITSGFEYETIWALGADAAIDDLDAIAYADREFDEVGIDSIETSVAV 359 Query: 352 ATAMELYEKGHIKDEELGDAPPFRWGNTEVLHYYIEKIAKREGFGDKLAEGSYRLAESYG 411 A AM DA WG+ + I++I + G L G+ + + YG Sbjct: 360 AVAM--------------DAGVIPWGDGKAALDLIKQIRQGTPLGRILGSGAAAVGQMYG 405 Query: 412 HPELSMTVKKLELPAYDPRGAEGHGLGYATNNRGGCHIKNYMISPEILGYPYKMDPHDVS 471 + + VK +PAYDPR +G GL YAT G H Y ++ IL +DP Sbjct: 406 LTRVPV-VKNQAIPAYDPRAVKGVGLTYATTPMGADHTAGYAVATNILRVGGFVDPLG-K 463 Query: 472 DDKIKMLILFQDLTALIDSAGLCLFTTFGL-----GADDYRDLLNAALGWDFTTEDYLKI 526 + ++++ Q TA +DS G+CLF F + G + D++NA T +D + Sbjct: 464 EGQVELSRNLQIATAAVDSTGMCLFIAFAILDIPDGFNALVDMINARYDLSLTGDDVTAL 523 Query: 527 GERIWNAERLFNLKAGLDPARDDTLPKRFLEEPMP 561 G+ I AE FN +AG A D LP+ F EEP P Sbjct: 524 GKTILKAELDFNRRAGFTSAH-DRLPE-FFEEPCP 556 Lambda K H 0.316 0.138 0.414 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: 939 Number of extensions: 48 Number of successful extensions: 8 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: 605 Length of database: 575 Length adjustment: 37 Effective length of query: 568 Effective length of database: 538 Effective search space: 305584 Effective search space used: 305584 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: 53 (25.0 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