Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate PP_2184 PP_2184 putative Formate dehydrogenase, beta subunit
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__Putida:PP_2184 Length = 525 Score = 319 bits (818), Expect = 2e-91 Identities = 190/523 (36%), Positives = 287/523 (54%), Gaps = 26/523 (4%) Query: 26 PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMI-YPEG 84 PC SV A GA +V A E E L ++ T G P++ +G Sbjct: 13 PCDSVAR-----AVGADQVAEALLREAERRQLPLDIQR--TSSRGLYWLEPLIECDSAQG 65 Query: 85 -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRE-SDIPFYKNQQRNILSE 142 + + + P DVP ++ L +P + AL +IP+ K QQR + + Sbjct: 66 RLGFGPITPHDVPSLLD-----------ALAGEPGGHSLALGPVEEIPYLKTQQRLLFAR 114 Query: 143 NLRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESR 202 S+DDY A GG++ L + + +V+ + S LRGRGG FPA KW R Sbjct: 115 AGITRPLSLDDYRANGGFAGLEAAV-ALDGAEVVAAVLDSGLRGRGGAAFPAGIKWRTVR 173 Query: 203 NAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPL 262 +A KYV+ NADEGD G F DR L+EG+P ++EG+II AVGA +G+IYVR EYP Sbjct: 174 DAGAGQKYVVCNADEGDSGTFADRMLMEGDPFLLIEGMIIAGLAVGADKGYIYVRSEYPD 233 Query: 263 AVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPR 322 A+ ++ A A + G++G D+ GSG F ++V +GAGA++CGE +AL+ ++EG+ G R Sbjct: 234 AIRVLDQAFAIARDAGYLGADVAGSGQAFDLEVRVGAGAYICGEETALLESIEGKRGIVR 293 Query: 323 PKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITN 382 K A++G++ P++++NV T A+V I+ KGA ++ +G S GT F L G I Sbjct: 294 AKPPLPALQGLFGLPTLVHNVLTLASVPIILAKGAAFYRDFGMGRSLGTMPFQLAGNIRQ 353 Query: 383 TGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAG 442 GLVE G+TLR+++ GGG G+ KA Q GGP G +P + D P+D++ G Sbjct: 354 GGLVERAFGLTLRELVEGYGGGTASGRPLKAAQVGGPLGAWVPPSHFDTPLDYEAFAAVG 413 Query: 443 SMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKG-- 500 +M+G GG++V D+ M +AR+ + F +ESCGKCTPCR G + + V+ R+ Sbjct: 414 AMLGHGGVVVADDTLNMASMARFALQFCAEESCGKCTPCRIGSTRGMEVVDRLIASSDIT 473 Query: 501 -KEGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541 + LL +L ++ +LCA+G PV S ++YF ++ Sbjct: 474 ERHDQALLLRDLCDTLQYGSLCAMGGMTAYPVASALKYFPADF 516 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: 842 Number of extensions: 51 Number of successful extensions: 3 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: 525 Length adjustment: 36 Effective length of query: 599 Effective length of database: 489 Effective search space: 292911 Effective search space used: 292911 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