GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Caulobacter crescentus NA1000

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__Caulo:CCNA_01648
          Length = 420

 Score =  155 bits (393), Expect = 2e-42
 Identities = 131/394 (33%), Positives = 188/394 (47%), Gaps = 39/394 (9%)

Query: 20  PAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIG-NGY 78
           P P +  RG  +RL  + G+E +D          G+ HP +  AL +Q     H+   G 
Sbjct: 27  PLPVVATRG--ARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHVMFGGL 84

Query: 79  TNEPALRLAKKLIDATFAE--RVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKN 136
            +EPA RLAK+L      +   VFF  SG+ A E A+K+A +Y  +R    ++  +AF+ 
Sbjct: 85  AHEPAYRLAKRLARLLPGDLDHVFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFRG 144

Query: 137 AFHGRTLFTVS------------AGGQPTYSQDFAPLPPDIRHAAYNDLNSASALIDDNT 184
            +HG TL T++            AG  P  +Q  A LP D   A+   L++  A      
Sbjct: 145 GYHGDTLATMTVCDPEEGMHSLFAGVMP--AQVIADLPRD--PASEAALDALLAARGHEI 200

Query: 185 CAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGV 243
            A++VEP +QG GG++P     L+ LR L D+H  LLIFDE+ TG GRTG L+A    GV
Sbjct: 201 AAMLVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLFAMQAAGV 260

Query: 244 TPDILTTAKAL-GGGFPIGAMLT---------TQDYASVMTPGTHGTTYGGNPLATAVAG 293
            PDI+T +KAL GG  P+ A +          + D A+ +    HG TY  NPLA A A 
Sbjct: 261 EPDIVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAAL---MHGPTYMANPLACAAAN 317

Query: 294 KVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTEFAGKAKL 353
             LD+         V +   A  E L       G+  ++R LG +   V++ E       
Sbjct: 318 ASLDLFEDGAWARDVARVSAALAEGLEPCRAGEGVV-DVRTLGAI--GVVEFEAPVPVSD 374

Query: 354 IAQEAAKAGVMVLIAGGDVVRFAPALNVSDEEIA 387
           +    A  GV +    G VV   PA    DE+++
Sbjct: 375 LCARFAALGVWIR-PMGKVVYLTPAFTTPDEDLS 407


Lambda     K      H
   0.320    0.137    0.413 

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: 423
Number of extensions: 28
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: 408
Length of database: 420
Length adjustment: 31
Effective length of query: 377
Effective length of database: 389
Effective search space:   146653
Effective search space used:   146653
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