GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Dinoroseobacter shibae DFL-12

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 3607873 Dshi_1281 Respiratory-chain NADH dehydrogenase domain 51 kDa subunit (RefSeq)

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__Dino:3607873
          Length = 565

 Score =  265 bits (678), Expect = 3e-75
 Identities = 145/395 (36%), Positives = 225/395 (56%), Gaps = 17/395 (4%)

Query: 147 DSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPD 206
           D +++  Y A GGY  L  +      E V  ++K+S LRG GG GFP+  KW   R  P 
Sbjct: 186 DYETLAAYRAEGGYGVLRDLRASGDWEVVQAQVKQSGLRGLGGAGFPSGTKWGFVRANPG 245

Query: 207 PIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVEN 266
           P +Y+ VN DEG+PG F DR  +E  PH  LEG++I A+AV A   +IY+R EYP  +E 
Sbjct: 246 P-RYLAVNGDEGEPGTFKDRHYLERVPHLFLEGMLIAAWAVEAERCYIYMRDEYPAVLEI 304

Query: 267 INLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYI 326
           +   I    E G              +++  GAGA++CGE SA++ ++EG+ G PR +  
Sbjct: 305 LRREIAALEEAGIAEPG--------HIELRRGAGAYICGEESAMIESIEGKRGMPRHRPP 356

Query: 327 HTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLV 386
           + A  G++  P++++NVET   + +I  +G +  ++       G + +S+ G++   G+ 
Sbjct: 357 YVAQVGLFGRPTLVHNVETLHWIARICREGPEVLSATTHNDRVGLRSYSVSGRVARPGVY 416

Query: 387 EVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMG 446
            +P G T+ DII    GG+  G  FKA Q GGPS G +P +  D+P+DFD L   G+ +G
Sbjct: 417 LLPAGSTILDIID-AAGGMAEGHVFKAFQPGGPSSGLLPASAADVPLDFDTLQPLGTFIG 475

Query: 447 SGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE 506
           S  ++V+ +     D A   + F +DESCG+CTPCR G  + + ++      + +  D  
Sbjct: 476 SAAVVVLSDQDRARDAALNMLRFFEDESCGQCTPCRVGCEKAVKLM------QAERWDAG 529

Query: 507 LLEELAES-TGAALCALGKSAPNPVLSTIRYFRDE 540
           LL EL  +   A++C LG++APNP+LSTI++F +E
Sbjct: 530 LLSELCTAMADASICGLGQAAPNPILSTIKHFPEE 564


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: 871
Number of extensions: 53
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: 565
Length adjustment: 37
Effective length of query: 598
Effective length of database: 528
Effective search space:   315744
Effective search space used:   315744
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