GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas stutzeri RCH2

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF4018 Psest_4091 diaminobutyrate--2-oxoglutarate aminotransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>FitnessBrowser__psRCH2:GFF4018
          Length = 425

 Score =  202 bits (513), Expect = 2e-56
 Identities = 134/408 (32%), Positives = 218/408 (53%), Gaps = 22/408 (5%)

Query: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNK--LTHTC-FQV 81
           P+    A+ A +   +G+ +IDF  G   LN GH HP +  A+ E +    +TH      
Sbjct: 19  PVVFNQAQGAELVTQDGKRYIDFLAGAGTLNYGHNHPVLKQALLEYIENDGITHGLDMYT 78

Query: 82  LAYEPYVELCEKI--NAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAY 139
            A E ++E   ++    +  GD+ +      TG+ AVE A+K+AR  TGR  +I+FT  +
Sbjct: 79  AAKERFLETFNRLILEPRGMGDY-RMQFTGPTGTNAVEAAMKLARKVTGRNNIISFTNGF 137

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPR 199
           HG ++  L  TG    +  G G+    + R  Y N     +  ++I  ++++  + +   
Sbjct: 138 HGCSIGALAATGNQ-HHRGGSGISLTDVSRMPYANYFGDKT--NTIGMMDKLLSDPSSGI 194

Query: 200 DI-AAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQM 258
           D  AA+I+E VQGEGG   A  E+M++L  LC +H +LLI D++Q G GRTGTFF+ E+M
Sbjct: 195 DKPAAVIVEVVQGEGGLNTASTEWMRKLEKLCRKHEMLLIVDDIQAGCGRTGTFFSFEEM 254

Query: 259 GVAADLTTFAKSIAG-GFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVF- 316
           G+  D+ T +KS++G G P A V  + E +D   PG   GT+ G+  A   A A +E F 
Sbjct: 255 GIQPDIVTLSKSLSGYGLPFAMVLLRQE-LDQWKPGEHNGTFRGNNHAFVTAAAAVEHFW 313

Query: 317 EEEHLLDRCKAVGERLVAGLKAIQKKY-PVIGDVRALGAMIAVELFENGDSHKPNAAAVA 375
           + +   +  KA G+R+  G++ I +++ P    ++  G MI +          P+    A
Sbjct: 314 QNDAFANSVKAKGKRIADGMQRIIRRHGPDSLYLKGRGMMIGISC--------PDGEIAA 365

Query: 376 QVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECFS 423
            V   A + GL++ + G +  V++ L PL   +EQ+DK LAIL++ F+
Sbjct: 366 AVCRHAFENGLVIETSGAHSEVVKCLCPLIISEEQIDKALAILDKAFA 413


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: 428
Number of extensions: 18
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: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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: 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