GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Dechlorosoma suillum PS

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase

Query= metacyc::MONOMER-11537
         (425 letters)



>FitnessBrowser__PS:Dsui_0023
          Length = 396

 Score =  179 bits (453), Expect = 2e-49
 Identities = 134/400 (33%), Positives = 200/400 (50%), Gaps = 36/400 (9%)

Query: 26  IFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYE 85
           +FA+  + + + D +G+ ++DF  G AV   GH HP I+ A+  Q  KL +        E
Sbjct: 24  VFAEG-RGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPS-PAFYNE 81

Query: 86  PYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA-----ATGRAGVIAFTGAYH 140
           P ++L   + A    D   +    +TG+EA E A+K+AR        G   +I F G +H
Sbjct: 82  PSLKLAAGLAAHSCFD---RVFFASTGAEANEGAIKLARKWGQKHKGGAHEIITFAGGFH 138

Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRD 200
           GRT+ T+  +GK    +     +PG  F     N+L      DS+A++            
Sbjct: 139 GRTLATMSASGKPGWDTLFAPQVPG--FPKAQLNDL------DSVAALIN--------ER 182

Query: 201 IAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGV 260
             AI++EP+QGEGG   A  EF++ LR +CD  G+LLI DEVQTG GRTG  FA +  G+
Sbjct: 183 TVAIMLEPIQGEGGVVPASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGI 242

Query: 261 TADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEH 320
             D+ T  K I GG PL+ +  K E +     G  GGTY G+P+  A   AV+EV     
Sbjct: 243 EPDIMTLGKGIGGGVPLSALLAK-ESVCCFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPG 301

Query: 321 LLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAQVVAK 380
            L    A GE L  GL+ +  +  + GE R  G + A+ L    D   P   A+ +   +
Sbjct: 302 FLAEVAAKGEYLGAGLQRLSDRLGLRGE-RGQGLLRALLL---ADERGP---AIVEAARE 354

Query: 381 ARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
              +GL+L +     ++LR +  LT    ++D+ LA +EE
Sbjct: 355 RGPEGLLLNA--PRPHLLRFMPSLTVSREEIDQMLAWLEE 392


Lambda     K      H
   0.320    0.137    0.394 

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: 431
Number of extensions: 25
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: 425
Length of database: 396
Length adjustment: 31
Effective length of query: 394
Effective length of database: 365
Effective search space:   143810
Effective search space used:   143810
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 (21.8 bits)
S2: 50 (23.9 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