GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Bacteroides thetaiotaomicron VPI-5482

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)

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



>lcl|FitnessBrowser__Btheta:350970 BT1442
           adenosylmethionine-8-amino-7-oxononanoate
           aminotransferase (NCBI ptt file)
          Length = 804

 Score =  149 bits (376), Expect = 3e-40
 Identities = 119/383 (31%), Positives = 196/383 (51%), Gaps = 29/383 (7%)

Query: 28  RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVMTNEPALR 86
           R +G+ I  ++GR  I+          G++HP L  A  DQ +K+ H+    +T++PA+ 
Sbjct: 410 RADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQAAKDQLDKMSHVMFGGLTHDPAIE 469

Query: 87  LAKTLCDLT--FAERVFFANSGAEANEAAFKLARRYAWEHHGK-EKNEIISFKNSFHGRT 143
           L K L  L     +++F+A+SG+ A E A K+A +Y W   GK +KN  ++ ++ +HG T
Sbjct: 470 LGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQY-WYAAGKPDKNNFVTIRSGYHGDT 528

Query: 144 LFTVSVG----------GQPKYLEGFEPAPGGIHHAEFNDLESV--KKLISK--EKTCAI 189
              +SV           G    +  F PAP      E+N  E +  ++ I K  ++  A+
Sbjct: 529 WNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFDGEWNPDEIIPLRETIEKHSKELAAL 588

Query: 190 VVEPI-QGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPD 248
           ++EPI QG GG+      +L+    LC E+D LL+FDE+ +G GR+G  +A++  GV PD
Sbjct: 589 ILEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLIFDEIATGFGRTGKLFAWEHAGVEPD 648

Query: 249 ILSSAKGLGGGF-PVAAMLTTAKVAASLG-----VGTHGSTYGGNALACAVAQRVVDTVS 302
           I+   K L GG+  ++A+L + ++A ++         HG T+ GN LACAVA   V  + 
Sbjct: 649 IMCIGKALTGGYMTLSAVLASNQIADTISNHAPKAFMHGPTFMGNPLACAVACASVRLLL 708

Query: 303 QPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLE 362
                + VK    +L++ +     ++    +VR  G  +G + TE+    A       +E
Sbjct: 709 DSGWAENVKRIEAQLKEELAP-ARKFPQVADVRILG-AIGVIQTERSVSMAY-MQRRFVE 765

Query: 363 EGVMVLVAGANVIRLAPSLIIPE 385
           EG+ V   G  V  + P +I PE
Sbjct: 766 EGIWVRPFGKLVYLMPPFIISPE 788


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: 675
Number of extensions: 33
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: 804
Length adjustment: 36
Effective length of query: 368
Effective length of database: 768
Effective search space:   282624
Effective search space used:   282624
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: 53 (25.0 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