GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas stutzeri RCH2

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF4233 Psest_4306 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= reanno::WCS417:GFF4238
         (406 letters)



>FitnessBrowser__psRCH2:GFF4233
          Length = 441

 Score =  149 bits (376), Expect = 2e-40
 Identities = 117/399 (29%), Positives = 185/399 (46%), Gaps = 44/399 (11%)

Query: 32  EGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFTNEPA-LRLA 90
           EG       GR+++D   G+     GH    +  A+++Q  K+          P    LA
Sbjct: 35  EGMYYTASDGRQVLDGTAGLWCCNAGHGRREISEAVSKQIAKMDFAPTFQMGHPLPFELA 94

Query: 91  HKL--IDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSE--KYEIIAALNSFHGRTL 146
            KL  I      RVFF NSG+E+ + A K+A  +A+ R   +  +  +I    ++HG   
Sbjct: 95  EKLAAISPEGLNRVFFTNSGSESADTALKIA--LAYQRAIGQGSRTRLIGRELAYHGVGF 152

Query: 147 FTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVS---------------------- 184
             ++VGG +     FGP + G+ H+P+  LD  + A S                      
Sbjct: 153 GGMSVGGMANNRRAFGPMLPGVDHLPHT-LDLQRNAFSRGLPQHGVERADELERLVTLHG 211

Query: 185 -DKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQH 243
            +   AV++EP+ G  GV+   + YLQ  R++   +  LL+FDEV TG GR G  FA Q 
Sbjct: 212 AENIAAVIVEPMSGSAGVILPPVGYLQRLREITAKHGILLIFDEVITGFGRVGEAFAAQR 271

Query: 244 YGVTPDILTSAKSL-GGGFPIAAMLTTEALAKHLVVGT-------HGTTYGGNPLACAVA 295
           +GVTPDILT AK L  G  P+ A+L  + L    + G        HG TY G+P+ACA A
Sbjct: 272 WGVTPDILTCAKGLTNGAIPMGAVLAADHLFDAFMKGPESVIEFFHGYTYSGHPVACAAA 331

Query: 296 EAVIDVINTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAK 355
            A   +     +          ++  L  +     +  ++R +GL+ G   +    G  K
Sbjct: 332 LATQQIYQQENLFQKAIDLEPYWQEALFSLRDLPNVI-DIRTVGLVAGIQFAAHADGVGK 390

Query: 356 ---DVFNAAEKENLMILQAGPDVVRFAPSLVVEDADIKE 391
              +VF    ++ L++  +G D +  +P+L+VE A+I +
Sbjct: 391 RGYEVFRECFEKGLLVRASG-DTIALSPALIVEKAEIDQ 428


Lambda     K      H
   0.320    0.137    0.400 

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: 465
Number of extensions: 27
Number of successful extensions: 6
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: 406
Length of database: 441
Length adjustment: 32
Effective length of query: 374
Effective length of database: 409
Effective search space:   152966
Effective search space used:   152966
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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