GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamH in Dechlorosoma suillum PS

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Dsui_3030 Dsui_3030 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__PS:Dsui_3030 Dsui_3030 NADH:ubiquinone
           oxidoreductase, NADH-binding (51 kD) subunit
          Length = 602

 Score =  288 bits (737), Expect = 5e-82
 Identities = 170/505 (33%), Positives = 261/505 (51%), Gaps = 45/505 (8%)

Query: 61  VNTKGTGCPGFCERGPIVMIYPEGICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATG 120
           V+   T C G C++GP +++                          + + RL ++     
Sbjct: 116 VSVDVTSCTGMCDQGPALLV------------------------NGRPITRLTHQRVNEI 151

Query: 121 TRALRESDIPFYKNQQRNILSENLRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIK 180
              +R         Q+   + +N+R     ++  L  G   A +  L    PE  +GE++
Sbjct: 152 CELIRSRRPLSLWPQEYFRVEDNIRRKDDLLNTVLEPGAALAAAMAL---GPEAWLGEVQ 208

Query: 181 KSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGL 240
           KS+LRGRGG GF    KWE  RNAP   + ++ NADEG+PG F DR L+   P  + EG+
Sbjct: 209 KSSLRGRGGAGFTTGVKWEACRNAPGEERVIVCNADEGEPGTFKDRVLLTSYPDHVFEGM 268

Query: 241 IIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGFVGKDILG-SGFDFTVKVHMGA 299
            + AYA GA +GF+Y+R EY   +E +  A+++  E G +G+ I G + FDF +++H+GA
Sbjct: 269 TLAAYATGARQGFLYLRGEYRYLLEPLEAALQRRREAGLLGQGIRGQASFDFDIEIHLGA 328

Query: 300 GAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADW 359
           GA+VCGE +AL+ +LEG+ G PR +     +KG    P+V+NNVET A    I  +GA+ 
Sbjct: 329 GAYVCGEETALIESLEGKRGTPRIRPPFPVIKGYLGRPTVVNNVETLAKTVLIALEGAER 388

Query: 360 FTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGP 419
           F + GTA STGTK+ S+ G     G+ E P GV++  I+        G    +AVQ GG 
Sbjct: 389 FAAVGTAQSTGTKLLSISGDCAFPGIYEYPFGVSIEQILEDC-----GATDVQAVQVGGA 443

Query: 420 SGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCT 479
           SG C+        + ++++  AGS M      + D    + ++AR F+ F   ESCG CT
Sbjct: 444 SGTCLASYEFHRGIAYEDVPTAGSFM------IFDTSRDLFEVARNFVHFFAHESCGFCT 497

Query: 480 PCREGIRQMLAVLTRITVGKGKE---GDIELLEELAESTGAALCALGKSAPNPVLSTIRY 536
           PCR G   +   + ++  G G +    DIE +  L ++  A+ C LG +A NPV+ T+  
Sbjct: 498 PCRVGTSLLRNFMDKLATGHGAKYDLADIEWINRLLKA--ASHCGLGLAAANPVVETLIK 555

Query: 537 FRDEYEAHIREKK-CPALSCKEMIA 560
           FR  YE  ++     PA    + +A
Sbjct: 556 FRPAYERRLQSLDFAPAFDLDQSLA 580


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: 931
Number of extensions: 52
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 635
Length of database: 602
Length adjustment: 37
Effective length of query: 598
Effective length of database: 565
Effective search space:   337870
Effective search space used:   337870
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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