GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Herbaspirillum seropedicae SmR1

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate HSERO_RS08845 HSERO_RS08845 NADH dehydrogenase

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__HerbieS:HSERO_RS08845
          Length = 431

 Score =  333 bits (853), Expect = 1e-95
 Identities = 173/415 (41%), Positives = 253/415 (60%), Gaps = 4/415 (0%)

Query: 139 ILSENLRLDSKSMDDYLAIGGYSALSKVLFQ-MTPEDVMGEIKKSNLRGRGGGGFPAWRK 197
           ++  +L  ++  ++DY+  GGY +L ++L + +TPE V+ ++K S LRGRGG GFP   K
Sbjct: 12  LILADLNGENWHLEDYVKRGGYESLKRILNEKITPEQVIADLKASGLRGRGGAGFPTGLK 71

Query: 198 WEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVR 257
           W          KY++ N DEG+PG F DR +I  NPH+++EG+IIG YA+G   G+ Y+ 
Sbjct: 72  WSFMPRQFPGQKYLVCNTDEGEPGTFKDRDIIRYNPHALIEGMIIGGYAMGITVGYNYIH 131

Query: 258 QEYPLAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGR 317
            E   A E    A+ +A   GF+G +ILG+GF F +  H G GA++CGE +AL+ +LEG+
Sbjct: 132 GEIFSAYERFEEALEEARAAGFLGDNILGTGFSFQLHAHHGYGAYICGEETALLESLEGK 191

Query: 318 AGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLV 377
            G+PR K    A  G++  P+ +NN ET+A V  I   G   +   G   + GTKIFS+ 
Sbjct: 192 KGQPRFKPPFPASFGLYGKPTTINNTETFAAVPFIFKVGPQAYAEMGKPNNGGTKIFSIS 251

Query: 378 GKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIP-EAMLDLPVDFD 436
           G +   G  E+P+G     ++ ++ GG+ GGKK KAV  GG S   I  + M+D  +D+D
Sbjct: 252 GDVERPGNYEIPLGTPFSTLL-ELAGGMRGGKKIKAVIPGGSSAPVIRGDVMMDTTMDYD 310

Query: 437 ELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRIT 496
            + KAGSM+GSG +IVMDE  CMV        F  +ESCG+CTPCREG   M  ++ RI 
Sbjct: 311 AIAKAGSMLGSGAVIVMDETRCMVKSLLRLSYFYYEESCGQCTPCREGTGWMYRMVERIE 370

Query: 497 VGKGKEGDIELLEELAES-TGAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKC 550
            G GK  D+++L  +A++  G  +CALG +A  PV + ++ FR+E+E HI  K C
Sbjct: 371 NGHGKMEDLDVLNSVADNIQGRTICALGDAAAMPVRAFVKNFREEFEYHIEHKHC 425


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: 749
Number of extensions: 33
Number of successful extensions: 5
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: 431
Length adjustment: 35
Effective length of query: 600
Effective length of database: 396
Effective search space:   237600
Effective search space used:   237600
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.

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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