Align aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) (characterized)
to candidate 206619 DVU1179 aldehyde:ferredoxin oxidoreductase, tungsten-containing
Query= BRENDA::Q51739 (605 letters) >MicrobesOnline__882:206619 Length = 576 Score = 284 bits (727), Expect = 6e-81 Identities = 208/579 (35%), Positives = 291/579 (50%), Gaps = 47/579 (8%) Query: 7 RFIRVNLSTGDIKVEEYDEELAKKWLGSRGLAIYLLLKEMDPTVDPLSPENKLIIAAGPL 66 R +R+N + EE + LG R L L+ E+ LS EN+++ A G L Sbjct: 3 RILRINTRERSWRFEEPGKYAG---LGGRSLTSRLVQDEVPADTHALSAENRIVAAIGLL 59 Query: 67 TGTSAPTGGRYNVVTKSPLTGFITMANSGGYFGAELKFAGYDAIVVEGKAEKP---VYIY 123 +GT A GR ++ KSPLTG I +NSGG F +L A+V+E K E V I Sbjct: 60 SGTGAANSGRISIGAKSPLTGGIKESNSGGSFCQKLARLDILALVLEDKPEPNAPLVNIV 119 Query: 124 IKDEHIEIRDASHIWGKKVSETEATIRKEVGSEKVKIASIGPAGENLVKFAAIMNDGH-- 181 + + + +A + GK + + G +K IGPAGE+L+ A+I Sbjct: 120 LTKDGVRFDEAGDMAGKGTYACMDAVSERYG-KKACAMLIGPAGESLLTGASIQFSDPWG 178 Query: 182 ---RAAGRGGVGAVMGSKNLKAIAV--EGSKTVPIADKQKFMLVVREKVNKLRNDPVAGG 236 RAAGRGG+GAVMGSK +KAI + EG AD+ +F + LR PV G Sbjct: 179 RPARAAGRGGLGAVMGSKRVKAIVIDDEGGTRFGYADEARFKAASKRWAEILRAHPVTGQ 238 Query: 237 GLPKYGTAVLVNIINENGLYPVKNFQTGVYPYAYEQSGEAMAAKYLVR-----NKPCYA- 290 GLP +GTA+LVNIINE G +P +NF+TG +A + SGE M A+Y+ + + C+A Sbjct: 239 GLPGFGTAILVNIINEAGAFPTQNFRTGRCEHAPKISGEVM-AEYMEKRGGKVKEGCHAG 297 Query: 291 CPIGCGRVNRLPTVGE--TEGPEYESVWALGANLGINDLASIIEANHMCDELGLDTISTG 348 C I C + N + GE T G EYE+VWA G N I D+ I + MCD+LG+DTI G Sbjct: 298 CIIQCSQ-NYVDPAGEYITSGFEYETVWAFGGNSLIADIDDIARLDRMCDDLGVDTIEIG 356 Query: 349 GTLATAMELYEKGHIKDEELGDAPPFRWGNTEVLHYYIEKIA-KREGFGDKLAEGSYRLA 407 T+A AM DA WG+ + + +IA + G + G A Sbjct: 357 NTVAIAM--------------DAGIIPWGDGKAALKLLARIADPSDALGRIIGSGVGFAA 402 Query: 408 ESYGHPELSMTVKKLELPAYDPRGAEGHGLGYATNNRGGCHIKNYMISPEILGYPYKMDP 467 +++G + TVK +PAYDPR A+G G+ YAT G H Y I +L ++P Sbjct: 403 QAFGIDRVP-TVKNQSMPAYDPRAAKGVGVTYATTTMGADHTAGYAICQNMLKVGGDVNP 461 Query: 468 HDVSDDKIKMLILFQDLTALIDSAGLCLFTTFGL-----GADDYRDLLNAALGWDFTTED 522 + +++ Q TA +DS GLCLF F + D+++A G DFT D Sbjct: 462 LG-KEGQVETSKALQVATATVDSLGLCLFVAFAVLDTPDAVQCICDMVSARHGIDFTPND 520 Query: 523 YLKIGERIWNAERLFNLKAGLDPARDDTLPKRFLEEPMP 561 ++ IG + E+ FN AG P DD LP EP+P Sbjct: 521 FIAIGTDVLKVEQKFNADAGFTP-EDDQLPAFMKREPLP 558 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: 887 Number of extensions: 47 Number of successful extensions: 7 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: 576 Length adjustment: 37 Effective length of query: 568 Effective length of database: 539 Effective search space: 306152 Effective search space used: 306152 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