GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas simiae WCS417

Align 4-aminobutyrate-pyruvate transaminase (EC 2.6.1.96) (characterized)
to candidate GFF2189 PS417_11165 omega amino acid--pyruvate aminotransferase

Query= BRENDA::Q7XN12
         (497 letters)



>FitnessBrowser__WCS417:GFF2189
          Length = 431

 Score =  268 bits (685), Expect = 3e-76
 Identities = 160/439 (36%), Positives = 245/439 (55%), Gaps = 14/439 (3%)

Query: 49  SMLAPFTAGWHSTDLEPLIIERSEGSYVYDSKGNKYLDTLAGLWCTALGGSEPRLVKAAT 108
           S+ APFTA     + +P++ +R+ G +   ++G   LD +AGLWC   G  +PR+V+A  
Sbjct: 4   SLWAPFTA-MRPFNRQPMLFDRAAGMHYTTTEGRDVLDAMAGLWCVNAGHGQPRIVEAIR 62

Query: 109 DQLNKLPFYHSFWNSTAKPPLDLAEELISMFTAKEMGKVFFTNSGSEANDSQVKLVWYYN 168
           +   +L F  SF   +    L LA++L++   A  + KVFFTNSGSEA D+ +K+   Y+
Sbjct: 63  EAAGRLDFVSSF-KMSHPAALTLADQLVAKAPAN-LDKVFFTNSGSEAVDTALKIARAYH 120

Query: 169 NALGRPNKKKIIAQSQAYHGSTLISASLSGLPAMHLKFDLPAPFVLHTDCPHYW--RFGL 226
            A G   + K+I +++ YHG      S+SG+      F      V H   P+    RF L
Sbjct: 121 QARGDSRRTKLIGRAKGYHGMGFGGLSVSGIGRQKRDFGPLLGDVAHLPLPYDAGSRFSL 180

Query: 227 PGEAEEEFATRLADNLENLILKEGPETVAAFIAEPVIGAGGVIPPPKTYFEKIQAVLQKY 286
               + E     AD L +L+    P TVAA I EPV G+GGV  PP  Y +K++ +  ++
Sbjct: 181 ---GQPEQGAHYADALLHLLEVHDPATVAAVIVEPVTGSGGVYAPPLGYLQKLREICDRH 237

Query: 287 DVLFIADEVITGFGRLGTMFGSDLYNIKPDLVSLAKALSSAYVPIGATLVSPEISDVVHS 346
            +L I DEVITGFGR+G  F ++ + + PDL++LAK L++  VP+G  LVS  + +    
Sbjct: 238 GLLLIFDEVITGFGRVGHGFAAEAFGVTPDLMTLAKGLTNGAVPMGGVLVSGAVYEAFMQ 297

Query: 347 QSNKIGFFAHGFTYSGHPVSCAVALEALKIYRERNIPAHVKQISPRFQEGIKAFAGSSII 406
              +     HG+TYS HP++CA  L  L+++ E  + AHV+QI+P +Q    A    +++
Sbjct: 298 GPEQAIELMHGYTYSAHPLACAAGLATLEVHEELGLNAHVRQIAPLWQNTALALREQALV 357

Query: 407 GETRGVGLLLATEFANNKSPNDPFPVEWGVAQIFGAECKKRGMLVKVVGDEIAMSPPLIM 466
            + R +GLL A E    +    P     GVAQ     C + G+LV+  G+ I +SPPLI+
Sbjct: 358 LDVRAIGLLCAVELKPREGA--PGARAAGVAQ----RCFEAGVLVRASGENIVLSPPLII 411

Query: 467 SQREVDGLVSIYGEALKAT 485
           +Q +V  + S  G+AL+AT
Sbjct: 412 NQEQVAQVFSTLGKALEAT 430


Lambda     K      H
   0.317    0.134    0.396 

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: 471
Number of extensions: 20
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: 497
Length of database: 431
Length adjustment: 33
Effective length of query: 464
Effective length of database: 398
Effective search space:   184672
Effective search space used:   184672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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