GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Chlorobium phaeobacteroides BS1

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 642684930 Cphamn1_2453 adenosylmethionine-8-amino-7-oxononanoate aminotransferase apoenzyme (EC 2.6.1.62)

Query= reanno::Marino:GFF3099
         (404 letters)



>IMG__ChlphaBS1_FD:642684930
          Length = 434

 Score =  154 bits (390), Expect = 4e-42
 Identities = 111/327 (33%), Positives = 169/327 (51%), Gaps = 27/327 (8%)

Query: 21  PGSIIPVRG-EGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NV 78
           P  + PV+G  G RI  ++GR  ID          G++HP L  A+  Q EK+ H+    
Sbjct: 25  PLPVYPVKGASGVRIELEDGRRLIDGMSSWWAAIHGYNHPVLNEAVRKQLEKMSHVMFGG 84

Query: 79  MTNEPALRLAKTLCDLTFA--ERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFK 136
            T+EPA+RLA+ L DLT    ++VFF++SG+ + E A K+A +Y       +KN +++ +
Sbjct: 85  FTHEPAVRLAEKLVDLTPGPLQKVFFSDSGSVSVEVAIKMALQYHHAAGRPKKNRLLTIR 144

Query: 137 NSFHGRTLFTVSVGGQPKYLEG----------FEPAPG-GIHHA----EFNDLESVKKLI 181
           + +HG T   +SV      + G          F  AP  G H         D     ++ 
Sbjct: 145 SGYHGDTFAAMSVCDPVTGMHGLFSGVLPQQLFAEAPACGFHDVWSDDSIGDFRRQVEMY 204

Query: 182 SKEKTCAIVVEPI-QGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240
            +E   A+++EP+ QG GG+      +L  +R+LCD  D LL+FDE+ +G GR+G  +A 
Sbjct: 205 HRE-IAAVILEPVVQGAGGMRFYSPEYLVRVRELCDRYDLLLIFDEIATGFGRTGKMFAL 263

Query: 241 QMYGVVPDILSSAKGLGGGF-PVAAMLTTAKVA-----ASLGVGTHGSTYGGNALACAVA 294
           +   VVPDIL   K L GG+  +AA LT   V+     A  GV  HG T+  N LACAVA
Sbjct: 264 EHADVVPDILCIGKALTGGYMTLAATLTNGDVSGVISNAEPGVFMHGPTFMANPLACAVA 323

Query: 295 QRVVDTVSQPEILKGVKARSDKLRKGM 321
              +D +++ +    V+    +L  G+
Sbjct: 324 SASIDLLAESDWRNSVRVIEAQLASGL 350


Lambda     K      H
   0.318    0.137    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: 460
Number of extensions: 15
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: 404
Length of database: 434
Length adjustment: 32
Effective length of query: 372
Effective length of database: 402
Effective search space:   149544
Effective search space used:   149544
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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