GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas simiae WCS417

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF4563 PS417_23355 4-aminobutyrate aminotransferase

Query= reanno::pseudo3_N2E3:AO353_11510
         (425 letters)



>FitnessBrowser__WCS417:GFF4563
          Length = 416

 Score =  348 bits (894), Expect = e-100
 Identities = 175/412 (42%), Positives = 256/412 (62%), Gaps = 4/412 (0%)

Query: 16  VPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKLT 75
           + + +  +HPI   H KN+ V D  G+ +IDF GGI VLN GH HP V+ A+ +Q  +LT
Sbjct: 6   ISQSISIVHPISLSHGKNAEVWDTSGKRYIDFVGGIGVLNLGHCHPGVVDAIRDQATRLT 65

Query: 76  HTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAGVIAF 135
           H  F    + PYVEL +++ A +P D+    +L  +G+EA EN++KI R ATGR  VIAF
Sbjct: 66  HYAFNAAPHAPYVELMDRLTAFIPVDYPISGMLTNSGAEAAENALKIVRGATGRTAVIAF 125

Query: 136 TGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKND 195
            GA+HGRT+ TL L GKV PY   +G++PG ++   YP+  +GV+  +++ +++R+F  +
Sbjct: 126 DGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVYHLPYPSADNGVTCAEALKAMDRLFSVE 185

Query: 196 AEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255
            +  D+A  IIEPVQGEGGF     EF + LR  C+++ ILLIADE+Q+G GRTG  FA 
Sbjct: 186 IDVSDVACFIIEPVQGEGGFLALDIEFAQALRRFCNENNILLIADEIQSGFGRTGERFAF 245

Query: 256 EQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEV 315
            ++G+  DL    KSIAGG PL  V G+   MD +  GGLGGTY+G+PIACAAALA ++ 
Sbjct: 246 SRLGIEPDLILLGKSIAGGVPLGAVVGRKALMDNLPKGGLGGTYSGNPIACAAALATLDA 305

Query: 316 FEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFENGDSHKPNAAA 373
             +EHL        E +V+  +  +A    P +G +  +G+M  +EL  N D   P    
Sbjct: 306 MTDEHLSAWGSQQEEAIVSRYQTWRAHGLTPYLGRLTGVGSMRGIEL-ANADG-TPAPKQ 363

Query: 374 VAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEECFSEL 425
           + +++  ARD GL+L+  G   +++R+L PLT     L++GL + E C  +L
Sbjct: 364 LTQLLGLARDAGLLLMPSGKSRHIIRLLAPLTIEPAVLEEGLTMFEACLKQL 415


Lambda     K      H
   0.320    0.137    0.395 

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: 482
Number of extensions: 17
Number of successful extensions: 2
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: 416
Length adjustment: 32
Effective length of query: 393
Effective length of database: 384
Effective search space:   150912
Effective search space used:   150912
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