GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:350970
          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:

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