GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Azospirillum brasilense Sp245

Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase

Query= curated2:Q3Z295
         (406 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS19630 AZOBR_RS19630
           4-aminobutyrate aminotransferase
          Length = 428

 Score =  226 bits (577), Expect = 8e-64
 Identities = 154/418 (36%), Positives = 218/418 (52%), Gaps = 42/418 (10%)

Query: 15  IPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHT 74
           +PVY        R E + LWD +G  +IDFAGGIAV   GH HP++ EA+  Q  +F HT
Sbjct: 22  MPVYVD------RAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHT 75

Query: 75  GNGYTN-EPVLRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSG 130
               T  E  + LA++L   +  +   +  F  +GAEA E A+K+AR  AH    + + G
Sbjct: 76  CAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIAR--AH----TGRPG 129

Query: 131 IVAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPDIRHAAYNDINSASALID-------- 181
           ++AF  AFHGRTL  ++  G+   Y   F P P ++ HA + +     ++ D        
Sbjct: 130 VIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQL 189

Query: 182 -----DAT--CAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGE 234
                DAT   A+IVEP+QGEGG   A   FLQ LR++CD +  LLI DE+QTG  RTG+
Sbjct: 190 FKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGK 249

Query: 235 LYAYMHYGVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGK 294
           ++A  H GV PDL+T AK+L GGFP+ A+    E       G  G TY G+PLA+  A  
Sbjct: 250 MFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALA 309

Query: 295 VLELINTPEMLNGVKQRHDWFVERLNTINHR--YGLFSEVRGLGLLIGCVLNAD------ 346
           VL++I   +++       +    R  T+  R    +  +VR LG +I   L  D      
Sbjct: 310 VLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEP 369

Query: 347 YAGQAKQISQEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAACEHFVS 402
            A   K +  +AA+ G+++L  G  GNV+R    L  S+  V  GLD    + E  VS
Sbjct: 370 AAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLEELVS 427


Lambda     K      H
   0.319    0.136    0.408 

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: 457
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: 406
Length of database: 428
Length adjustment: 31
Effective length of query: 375
Effective length of database: 397
Effective search space:   148875
Effective search space used:   148875
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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