GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Caulobacter crescentus NA1000

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase

Query= SwissProt::P50457
         (421 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02326 CCNA_02326 acetylornithine
           aminotransferase/succinyldiaminopimelate
           aminotransferase
          Length = 405

 Score =  181 bits (460), Expect = 3e-50
 Identities = 140/403 (34%), Positives = 189/403 (46%), Gaps = 44/403 (10%)

Query: 27  QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTA--YQIVPYES 84
           +    A L   EG EY+D  AGIA    GH HP LV  ++ Q ++  H +  Y+I   E 
Sbjct: 26  ERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNIYRIPEQEE 85

Query: 85  YVTLAEKINALAPVSGQAKTAFFT-TGAEAVENAVKIARAH---TGRP---GVIAFSGGF 137
              LA+ + A    +  A   FFT +G EAVE A+K AR +    G+P    +  F G F
Sbjct: 86  ---LADALCA----NSFADVVFFTNSGTEAVECALKTARKYHSANGQPERIDIYGFDGSF 138

Query: 138 HGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAK 197
           HGRTY  +  +G  + Y  GFGP       +P  S L    T    DAI    K+ I + 
Sbjct: 139 HGRTYAAVNASGNPS-YVDGFGP------RLPGYSQL----TFGDHDAI----KAAIASP 183

Query: 198 QVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMD-HY 256
             AAII EPVQGEGG    P + +  +R+LCDEHG+++I DEVQ G  RTGKLFA +   
Sbjct: 184 TTAAIIVEPVQGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAE 243

Query: 257 ADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDK 316
             +P +M +AK+L GG P+   +              G T+ GNPLA+A   A L II  
Sbjct: 244 GGEPHIMAVAKALGGGFPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAALEIIKS 303

Query: 317 ESLCERANQLGQRLKNTLIDAKESVP-AIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQ 375
               +    +       L   K+  P  I  VRG G +I V+            I     
Sbjct: 304 PETLDNVKTVSGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKL-----------IPNNRD 352

Query: 376 QRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDA 418
              LA+   LL  G   N +R L PL +   +   A+  L+ A
Sbjct: 353 FMVLARDEKLLIAGGGDNCVRLLPPLNLTIEEASEAIAKLEKA 395


Lambda     K      H
   0.319    0.134    0.388 

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: 411
Number of extensions: 19
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: 421
Length of database: 405
Length adjustment: 31
Effective length of query: 390
Effective length of database: 374
Effective search space:   145860
Effective search space used:   145860
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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