GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Pseudomonas fluorescens FW300-N2E2

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Pf6N2E2_1468 NAD-dependent formate dehydrogenase beta subunit

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1468
          Length = 519

 Score =  335 bits (860), Expect = 2e-96
 Identities = 194/511 (37%), Positives = 289/511 (56%), Gaps = 21/511 (4%)

Query: 38  ASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGIC--YLKVKPEDV 95
           A GA +V  A   E E   L   V    T   G     P+V +   G+   +  V P DV
Sbjct: 14  AVGADKVADALALEAERRQLPLTVLR--TSSRGLYWLEPLVELESAGVRLGFGPVTPADV 71

Query: 96  PEIVSHTIKEKKVVDRLLYEDPATGTRALRESD-IPFYKNQQRNILSENLRLDSKSMDDY 154
           P ++             L  DP +   AL   + IP+ K+QQR + +        S+DDY
Sbjct: 72  PGLLD-----------ALTGDPGSHPLALGPVEAIPYLKSQQRLLFARAGITQPLSLDDY 120

Query: 155 LAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIVN 214
            A GG+  L++ + QM   DV+  +  S LRGRGG  FPA  KW   R+A    KYV+ N
Sbjct: 121 RAQGGFQGLARSI-QMDGADVVASVLDSGLRGRGGAAFPAGIKWRTVRDAVGAQKYVVCN 179

Query: 215 ADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQA 274
           ADEGD G F DR L+EG+P  ++EG+II   AVGA  G+IYVR EYP A+  +N A+R A
Sbjct: 180 ADEGDSGTFADRMLMEGDPFLLIEGMIIAGLAVGATMGYIYVRSEYPAAISTLNDALRIA 239

Query: 275 SERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVW 334
            + G++G ++ GSG  F ++V +GAGA++CGE +AL+ +LEG+ G  R K    A++G++
Sbjct: 240 RDAGYLGANVSGSGRTFDIEVRVGAGAYICGEETALLESLEGKRGTVRAKPPLPAIQGLF 299

Query: 335 DHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTL 394
             P++++NV T A+V  I+ KGA ++  +G   S GT  F L G +   GLVE   G++L
Sbjct: 300 GLPTLVHNVVTLASVPIILEKGAQFYRDFGMGRSLGTMPFQLAGNVRQGGLVERAFGLSL 359

Query: 395 RDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMD 454
           R+++   GGG   G+  KA Q GGP G  +P +  D P+D++     G+M+G GG++V D
Sbjct: 360 RELVEGYGGGTASGRPLKAAQVGGPLGAWVPPSQFDTPLDYEAFAAMGAMLGHGGVVVAD 419

Query: 455 EDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRI---TVGKGKEGDIELLEEL 511
           +   M  +AR+ + F  +ESCGKCTPCR G  + + V+ R+   T    ++    LL++L
Sbjct: 420 DSLDMAQMARFALQFCAEESCGKCTPCRIGSTRGVEVVDRLIASTEAGARQEQALLLQDL 479

Query: 512 AESTG-AALCALGKSAPNPVLSTIRYFRDEY 541
            ++    +LCALG     PV S +++F  ++
Sbjct: 480 CDTLQYGSLCALGGMTSYPVASALKHFPADF 510


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: 790
Number of extensions: 44
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: 519
Length adjustment: 36
Effective length of query: 599
Effective length of database: 483
Effective search space:   289317
Effective search space used:   289317
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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