Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate RR42_RS05535 RR42_RS05535 NADH dehydrogenase
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Cup4G11:RR42_RS05535 Length = 431 Score = 328 bits (841), Expect = 3e-94 Identities = 169/409 (41%), Positives = 253/409 (61%), Gaps = 6/409 (1%) Query: 151 MDDYLAIGGYSALSKVLFQ-MTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIK 209 +DDY+ GGY L ++L + +TPE V+ ++K S LRGRGG GFP KW K Sbjct: 24 LDDYVKRGGYQQLKRILTEKITPEQVIADVKASGLRGRGGAGFPTGLKWSFMPRQFPGQK 83 Query: 210 YVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINL 269 Y++ N DEG+PG F DR +I NPH+++EG+ IGAYA+G G+ Y+ E + Sbjct: 84 YLVCNTDEGEPGTFKDRDIIRYNPHALIEGMAIGAYAMGITVGYNYIHGEIWNEYKIFEQ 143 Query: 270 AIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTA 329 A+ +A GF+G +ILGSGFDF + H G GA++CGE +AL+ +LEG+ G+PR K A Sbjct: 144 ALEEARAAGFLGDNILGSGFDFQLHAHHGYGAYICGEETALLESLEGKKGQPRFKPPFPA 203 Query: 330 VKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVP 389 G++ P+ +NN ET+A V +++ G + + G + G+KIFS+ G + G E+P Sbjct: 204 SFGLYGKPTTINNTETFAAVPFLLSIGPENYLKMGKPNNGGSKIFSISGDVERPGNYEIP 263 Query: 390 MGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIP-EAMLDLPVDFDELTKAGSMMGSG 448 +G ++ ++ GG+ GGK+ KAV GG S +P + M+ +D+D + KAGSM+GSG Sbjct: 264 LGTPFATLL-ELAGGMRGGKRIKAVIPGGSSAPVVPGDMMMASDMDYDSIAKAGSMLGSG 322 Query: 449 GMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELL 508 +IVMDE CMV F +ESCG+CTPCREG + ++ RI G+G++ D++LL Sbjct: 323 AVIVMDETRCMVRSLLRLSYFYFEESCGQCTPCREGTGWLYRMVNRIEHGEGRQEDLDLL 382 Query: 509 EELAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKC--PALS 554 +AE+ G +CALG +A PV ++++ E+E H+ K+C PA S Sbjct: 383 NNVAENIMGRTICALGDAAAMPVRGMLKHYWKEFEYHVEHKQCMVPAYS 431 Lambda K H 0.319 0.138 0.420 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: 733 Number of extensions: 29 Number of successful extensions: 5 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: 635 Length of database: 431 Length adjustment: 35 Effective length of query: 600 Effective length of database: 396 Effective search space: 237600 Effective search space used: 237600 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 (21.7 bits) S2: 52 (24.6 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