Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate GFF1614 HP15_1573 formate dehydrogenase, beta subunit
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Marino:GFF1614 Length = 571 Score = 288 bits (737), Expect = 5e-82 Identities = 157/394 (39%), Positives = 233/394 (59%), Gaps = 17/394 (4%) Query: 149 KSMDDYLAIGGYSALSKVLF-QMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDP 207 + + DY + GGY L ++T + + E++ + LRG GG GFP +RKW+ R P P Sbjct: 183 QKLADYRSAGGYQLLKDCREGRVTVDSLAEELEHAGLRGLGGAGFPTYRKWQAVRAEPGP 242 Query: 208 IKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENI 267 +Y ++NADEG+PG F DR +E PH LEG ++ A+AV A +IY+R EYP + + Sbjct: 243 -RYAVINADEGEPGTFKDRYYLEREPHGFLEGALVSAWAVEAQALYIYLRDEYPGLLVVL 301 Query: 268 NLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIH 327 AI + G I+ GF V + GAGA++CGE SAL+ +LEG+ G+PR + Sbjct: 302 KDAIAELETAG-----IVEPGF---VILRRGAGAYICGEESALIESLEGKPGKPRHRPPF 353 Query: 328 TAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVE 387 A KG++ P+++NNVET + +I +GA+W+ S G G G + FS+ G++ G+ Sbjct: 354 VAQKGLFGQPTLVNNVETVYWIPRIHAQGAEWYASQGRHGRKGLRSFSVSGRVARPGVHV 413 Query: 388 VPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGS 447 P GVTL ++I + GG+ G + A GG SGG +P + D+P+DFD L + G +GS Sbjct: 414 APAGVTLNELIEEYCGGMAEGHRLVAYLPGGASGGILPASKADIPLDFDTLQEHGCFIGS 473 Query: 448 GGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIEL 507 +IV+ + + A + F DESCG+CTPCR G +ML +L R T D + Sbjct: 474 AAVIVLSDQDDLQAAAANLLGFFADESCGQCTPCRVGTEKMLTLLERDT------WDEQT 527 Query: 508 LEELAE-STGAALCALGKSAPNPVLSTIRYFRDE 540 L++LA A++C LG++APNPVLS +R FR E Sbjct: 528 LQQLAAVMADASICGLGQAAPNPVLSLLRDFRSE 561 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: 824 Number of extensions: 40 Number of successful extensions: 4 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: 571 Length adjustment: 37 Effective length of query: 598 Effective length of database: 534 Effective search space: 319332 Effective search space used: 319332 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: 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