GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Pseudomonas fluorescens FW300-N1B4

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Pf1N1B4_2989 NAD-dependent formate dehydrogenase beta subunit

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2989
          Length = 520

 Score =  317 bits (813), Expect = 6e-91
 Identities = 188/522 (36%), Positives = 283/522 (54%), Gaps = 24/522 (4%)

Query: 26  PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMI-YPEG 84
           PC S+       A GA EV  A  T+     L  ++    T   G     P++ +  P+G
Sbjct: 8   PCDSLAR-----AVGADEVSVALATQARERNLPLDLQR--TSSRGLYWLEPLLEVDSPQG 60

Query: 85  -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSEN 143
            I +  +   DVP           V+D L  E  A         ++P+ K QQR + +  
Sbjct: 61  RIGFGPLTAADVPS----------VLDALQGEPSAHPLALGLVEELPYLKTQQRLLFARA 110

Query: 144 LRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRN 203
                 S++DY A GG+  L++ +  +  E     +  S LRGRGG  FPA  KW   R 
Sbjct: 111 GITQPLSLEDYRAHGGFEGLTQAI-ALGGEQTATAVFDSGLRGRGGAAFPAGIKWRTVRG 169

Query: 204 APDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLA 263
                KY++ NADEGD G F DR L+EG+P  ++EG+ I    VGA  G+IYVR EYP A
Sbjct: 170 TQAAQKYIVCNADEGDSGTFADRMLMEGDPFLLIEGMAIAGITVGATYGYIYVRSEYPDA 229

Query: 264 VENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRP 323
           V  +  A+  A   G++G ++ GSG  F ++V +GAGA++CGE +AL+ +LEG+ G  R 
Sbjct: 230 VATLRAALNIARSAGYLGANVGGSGQAFDMEVRVGAGAYICGEETALLDSLEGKRGIVRA 289

Query: 324 KYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNT 383
           K    A++G++  P++++NV T A+V  I+ KGA ++  YG   S GT  F L G I + 
Sbjct: 290 KPPIPALQGLFGLPTLVHNVLTLASVPLILAKGAQFYRDYGMGRSLGTMPFQLAGNIRHG 349

Query: 384 GLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGS 443
           GLVE   G+TLR+++   GGG   G+  KA Q GGP G  +P A  D P+D++     G+
Sbjct: 350 GLVERAFGLTLRELVEDYGGGTASGRPLKAAQVGGPLGAWVPPAQFDTPLDYEAFAAIGA 409

Query: 444 MMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVG---KG 500
           M+G GG++V D+   M  +AR+ + F  +ESCGKCTPCR G  + + V+ R+        
Sbjct: 410 MLGHGGVVVADDTLDMAHMARFAMQFCAEESCGKCTPCRIGSTRGVEVIDRLLAAPDQNS 469

Query: 501 KEGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541
           ++  + +L++L ++    +LCALG     PV S ++YF  ++
Sbjct: 470 RDEQVIILKDLCDTLQYGSLCALGGMTSYPVASALKYFPADF 511


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: 806
Number of extensions: 36
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: 520
Length adjustment: 36
Effective length of query: 599
Effective length of database: 484
Effective search space:   289916
Effective search space used:   289916
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