GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Dinoroseobacter shibae DFL-12

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__Dino:3609962
          Length = 413

 Score =  176 bits (445), Expect = 2e-48
 Identities = 133/402 (33%), Positives = 194/402 (48%), Gaps = 26/402 (6%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL-THYAFNAAP 73
           P+ +  G    +WD  G+RY+D    +   ++GHC+P VV+AI  QA  L TH  +    
Sbjct: 23  PLHIVRGEGVWLWDAGGRRYLDCYNNVP--HVGHCHPRVVDAIARQARVLNTHTRYL--- 77

Query: 74  HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRT 133
           H   L  +E+L+  +      A +L  +G+EA + AL++AR ATGK  +IA D  +HG T
Sbjct: 78  HEGVLDYIERLTGTMDNGLDQA-LLVCTGSEAVDVALRMARAATGKTGLIATDNTYHGNT 136

Query: 134 LATLNLNGKVAP---YKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED 190
            A   L+ +  P   Y   V  +P      P P  D         +A   L   E A   
Sbjct: 137 TAVAQLSTRRPPIGGYSDHVRLVPA-----PEPGTDGAAFGAHVARAAAEL---ETAGHG 188

Query: 191 VAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF-AFPRLG 249
           VAA I  P+    G   L   F +        RG L+I DE+Q GFGR G  F  +  LG
Sbjct: 189 VAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGYQALG 248

Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKG-GLGGTYSGNPISCAAALASLAQMTD 308
           I PD++ L KS+  G P+  VV R E+M A  +  G   T+ G+P++ AAA+A L  + D
Sbjct: 249 IAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAMAVLDVLED 308

Query: 309 ENLATWGERQEQAIVSRYERWKASGL-SPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367
           E L    +R     V RY   +   L  P I  + G G    ++  + DG+P  A  A V
Sbjct: 309 EGLVENAKR-----VGRYTLERLQALRHPAIDGVRGYGLAFALDLVDTDGAPNTALAAAV 363

Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILE 409
            E A+ R +L+   G+  HI+++  PL    E  +   D+L+
Sbjct: 364 TEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGDRLGDVLQ 405


Lambda     K      H
   0.320    0.137    0.402 

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: 475
Number of extensions: 28
Number of successful extensions: 7
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: 416
Length of database: 413
Length adjustment: 31
Effective length of query: 385
Effective length of database: 382
Effective search space:   147070
Effective search space used:   147070
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