GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Algiphilus aromaticivorans DG1253

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_043771338.1 U743_RS05875 acetylornithine/succinylornithine family transaminase

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_000733765.1:WP_043771338.1
          Length = 408

 Score =  245 bits (625), Expect = 2e-69
 Identities = 144/386 (37%), Positives = 202/386 (52%), Gaps = 6/386 (1%)

Query: 19  NYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSR 78
           NY P   V  RGEG  VW  DG   +D     +  S GHCHP+++AA+ EQA  L   S 
Sbjct: 21  NYAPADFVPVRGEGARVWTADGRELIDLGGGIAVNSLGHCHPELIAALTEQAGMLWHVSN 80

Query: 79  AFHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVC 138
              N       E++ A T + +    NSGAEA E+A+K  R++     G  + + EI+  
Sbjct: 81  VVTNVPALALAEKLCAETFAERAFFCNSGAEANEAALKLARRYASLKHG--EHKHEIVSF 138

Query: 139 ADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQG 198
           +++FHGRTL  V     P+   HFGP   G R +P+ D AA E AI P T A +VEP+QG
Sbjct: 139 SNSFHGRTLFTVSVGGQPKYSEHFGPLPGGIRHLPYNDIAAAEAAIGPQTCAVIVEPLQG 198

Query: 199 EAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKAL 258
           E GV+     +   +R  C  ++ +LV DE+Q+G+GRTG L A     +  DV    K L
Sbjct: 199 EGGVMPADPAFLAALRAACDRHDALLVFDEVQSGVGRTGSLYAYMQTEVTPDVLSTAKGL 258

Query: 259 AGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGA 318
            GGF P+ A+L+  E+   L  G HG+TFGGNPL CAVA+  + ++ E   +    ++G 
Sbjct: 259 GGGF-PIGAMLTTAEIAAYLPAGTHGTTFGGNPLGCAVAKRVLDIITEPDFLHGVQQRGL 317

Query: 319 RLLEGLKDI--RANTVREVRGRGLML-AVELHPEAGRARRYCEALQGKGILAKDTHGHTI 375
            +   L+D+  R      VRG GL+L AV   P  GRA     A Q  G+         +
Sbjct: 318 AMRAALQDMAARHGIFAGVRGSGLLLGAVTAEPWRGRAGEIVRAGQAAGVWCLVAGPDVV 377

Query: 376 RIAPPLVITSDEVDWALEQFATTLTQ 401
           R APPL I   E+   L +  + L++
Sbjct: 378 RFAPPLNIDEAELQDGLARLDSALSK 403


Lambda     K      H
   0.319    0.136    0.405 

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: 448
Number of extensions: 17
Number of successful extensions: 4
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: 404
Length of database: 408
Length adjustment: 31
Effective length of query: 373
Effective length of database: 377
Effective search space:   140621
Effective search space used:   140621
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 24 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