GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS19630
          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:

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