GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Marinobacter adhaerens HP15

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate GFF1614 HP15_1573 formate dehydrogenase, beta subunit

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__Marino:GFF1614
          Length = 571

 Score =  288 bits (737), Expect = 5e-82
 Identities = 157/394 (39%), Positives = 233/394 (59%), Gaps = 17/394 (4%)

Query: 149 KSMDDYLAIGGYSALSKVLF-QMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDP 207
           + + DY + GGY  L      ++T + +  E++ + LRG GG GFP +RKW+  R  P P
Sbjct: 183 QKLADYRSAGGYQLLKDCREGRVTVDSLAEELEHAGLRGLGGAGFPTYRKWQAVRAEPGP 242

Query: 208 IKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENI 267
            +Y ++NADEG+PG F DR  +E  PH  LEG ++ A+AV A   +IY+R EYP  +  +
Sbjct: 243 -RYAVINADEGEPGTFKDRYYLEREPHGFLEGALVSAWAVEAQALYIYLRDEYPGLLVVL 301

Query: 268 NLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIH 327
             AI +    G     I+  GF   V +  GAGA++CGE SAL+ +LEG+ G+PR +   
Sbjct: 302 KDAIAELETAG-----IVEPGF---VILRRGAGAYICGEESALIESLEGKPGKPRHRPPF 353

Query: 328 TAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVE 387
            A KG++  P+++NNVET   + +I  +GA+W+ S G  G  G + FS+ G++   G+  
Sbjct: 354 VAQKGLFGQPTLVNNVETVYWIPRIHAQGAEWYASQGRHGRKGLRSFSVSGRVARPGVHV 413

Query: 388 VPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGS 447
            P GVTL ++I +  GG+  G +  A   GG SGG +P +  D+P+DFD L + G  +GS
Sbjct: 414 APAGVTLNELIEEYCGGMAEGHRLVAYLPGGASGGILPASKADIPLDFDTLQEHGCFIGS 473

Query: 448 GGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIEL 507
             +IV+ +   +   A   + F  DESCG+CTPCR G  +ML +L R T       D + 
Sbjct: 474 AAVIVLSDQDDLQAAAANLLGFFADESCGQCTPCRVGTEKMLTLLERDT------WDEQT 527

Query: 508 LEELAE-STGAALCALGKSAPNPVLSTIRYFRDE 540
           L++LA     A++C LG++APNPVLS +R FR E
Sbjct: 528 LQQLAAVMADASICGLGQAAPNPVLSLLRDFRSE 561


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: 824
Number of extensions: 40
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: 571
Length adjustment: 37
Effective length of query: 598
Effective length of database: 534
Effective search space:   319332
Effective search space used:   319332
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.

Links

Downloads

Related tools

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