Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 200200 SO1017 NADH dehydrogenase I, F subunit (NCBI ptt file)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__MR1:200200 Length = 461 Score = 314 bits (805), Expect = 5e-90 Identities = 165/405 (40%), Positives = 239/405 (59%), Gaps = 13/405 (3%) Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW-----EESRNAP 205 +++Y GY A+ K L QM+P++++ +K + L+GRGG GFP KW +ES N Sbjct: 40 LEEYQTKQGYDAVRKALGQMSPDEIVSTVKDAGLKGRGGAGFPTGVKWGLMPKDESMN-- 97 Query: 206 DPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVE 265 I+Y++ NADE +P + DR L+E PH ++EG+II A A+ A+ G+I++R EY A Sbjct: 98 --IRYLLCNADEMEPNTWKDRLLMEQLPHLLIEGMIISAKALKAYRGYIFLRGEYVDAAI 155 Query: 266 NINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKY 325 N+ A+ +A G +GK+ILGSGFDF + VH GAG ++CGE +AL+ +LEGR PR K Sbjct: 156 NLRRAVEEAKAAGLLGKNILGSGFDFELFVHTGAGRYICGEETALINSLEGRRANPRAKP 215 Query: 326 IHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGST--GTKIFSLVGKITNT 383 AV GVW P+ +NNVET NV II G W+ + GS GTK+ GK+ N Sbjct: 216 PFPAVSGVWGKPTCVNNVETLCNVPAIIGNGVAWYHTLALPGSEDHGTKLMGFSGKVNNP 275 Query: 384 GLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGS 443 G+ E+P G+T R++ GG+ G + KA Q GG G + LD + + K G+ Sbjct: 276 GVWELPFGITARELFEGYAGGMRSGYRLKAWQPGGAGTGFLLPEHLDAQMYTAGIGKVGT 335 Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEG 503 MG+G + +D+ MV + R +F ESCG CTPCR+G+ + +L + G+G+EG Sbjct: 336 RMGTGLAMAVDDSISMVSLLRNMEEFFARESCGWCTPCRDGLPWSVKLLRSLERGEGQEG 395 Query: 504 DIELLEELAE--STGAALCALGKSAPNPVLSTIRYFRDEYEAHIR 546 D+ LE+L G CA A P+ S I+YFR E+EA I+ Sbjct: 396 DLATLEQLCNFLGPGKTFCAHAPGAVEPLASAIKYFRSEFEAGIK 440 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: 783 Number of extensions: 47 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: 461 Length adjustment: 35 Effective length of query: 600 Effective length of database: 426 Effective search space: 255600 Effective search space used: 255600 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