GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Klebsiella michiganensis M5al

Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= curated2:Q3Z295
         (406 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26375 BWI76_RS26375 aspartate
           aminotransferase family protein
          Length = 421

 Score =  229 bits (584), Expect = 1e-64
 Identities = 145/395 (36%), Positives = 204/395 (51%), Gaps = 33/395 (8%)

Query: 27  RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTN-EPVLR 85
           + E + LWD +G E IDFA GIAV   GH HP++  A+ +Q   F HT       E  + 
Sbjct: 28  KAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQIVPYESYVT 87

Query: 86  LAKKLIDATFAD---RVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRT 142
           LA+++      D   +  F  +GAEA E A+K+AR +      + + G++ F   FHGRT
Sbjct: 88  LAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAY------TGRPGLITFGGGFHGRT 141

Query: 143 LFTVSAGGQPA-YSQDFAPLPPDIRHAAY----NDINSASALID-----------DATCA 186
             T++  G+ A Y   F P P  + HA Y    + I +A A+             D   A
Sbjct: 142 FMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTADAMKSLDRIFKADIAADQVAA 201

Query: 187 VIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHYGVTPD 246
           +++EPIQGEGG   A   F+Q LR LCD H  LLI DEVQTG  RTG+L+A  HY V PD
Sbjct: 202 IVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPD 261

Query: 247 LLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLN 306
           L+T AK+L GGFP+  ++   E       G  G TY GNPLA A A  VL++I   ++  
Sbjct: 262 LMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQ 321

Query: 307 GVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ-----AKQISQEAAKA 361
             ++      E LN         ++VRG G ++    N    G+      +QI Q+A + 
Sbjct: 322 RAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEFNDPQTGEPSAEITRQIQQKAQEN 381

Query: 362 GVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFA 394
           G+++L  G  GNV+RF   L + + + T  LD  A
Sbjct: 382 GLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILA 416


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: 448
Number of extensions: 21
Number of successful extensions: 6
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: 421
Length adjustment: 31
Effective length of query: 375
Effective length of database: 390
Effective search space:   146250
Effective search space used:   146250
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