GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Shewanella oneidensis MR-1

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 200475 SO1300 glutamate-1-semialdehyde-2,1-aminomutase (NCBI ptt file)

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__MR1:200475
          Length = 430

 Score =  141 bits (356), Expect = 3e-38
 Identities = 102/336 (30%), Positives = 163/336 (48%), Gaps = 27/336 (8%)

Query: 21  APFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN--GY 78
           +P    + +G+ ++D  GK YID+ G      LGH HP++REA+        H G   G 
Sbjct: 32  SPLFIEKADGAYIYDADGKAYIDYVGSWGPMILGHNHPKIREAVLAAV----HNGLSFGA 87

Query: 79  TNEPVLRLAKKLIDATFA-DRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137
             E  +++A+K+I    + ++V   +SG EA  +A++LAR F      +++  I+ F+  
Sbjct: 88  PTELEVQMAEKVIAMVPSIEQVRMVSSGTEATMSAIRLARGF------TNRDKILKFEGC 141

Query: 138 FHGRT--LFTVSAGGQPAYSQDFAP-LPADI-RH---AAYNDINSASALIDD---STCAV 187
           +HG    L   +  G     Q  +P +P D  +H   A YND++S  +L +        +
Sbjct: 142 YHGHADCLLVKAGSGALTLGQPSSPGIPEDFAKHTLTAVYNDLDSVRSLFEQYPTEISCI 201

Query: 188 IVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDL 247
           I+EP+ G    +P    FL+GLR LC+   ALLI DEV TG  R  +  A  HYGVTPDL
Sbjct: 202 IIEPVAGNMNCIPPIPGFLEGLRSLCDEFGALLIIDEVMTGF-RVSKSGAQGHYGVTPDL 260

Query: 248 LTTAKALGGGFPVGALLATEECAR-VMTVGT--HGTTYGGNPLASAVAGKVLELINTPEM 304
            T  K +GGG PVGA    ++  + +   G      T  GNP+A +     +E +    +
Sbjct: 261 TTLGKVIGGGMPVGAFGGRKDVMQFIAPTGPVYQAGTLSGNPIAMSAGLAQMEALCEEGL 320

Query: 305 LNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIG 340
              +  +     E       ++G+   +  +G + G
Sbjct: 321 YEALSAKTKRIAEGFKAAADKHGIPMAINYVGGMFG 356


Lambda     K      H
   0.319    0.135    0.406 

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: 422
Number of extensions: 24
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: 406
Length of database: 430
Length adjustment: 32
Effective length of query: 374
Effective length of database: 398
Effective search space:   148852
Effective search space used:   148852
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