GapMind for catabolism of small carbon sources

 

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

Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)

Query= SwissProt::Q6CWC1
         (437 letters)



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

 Score =  161 bits (408), Expect = 6e-44
 Identities = 123/417 (29%), Positives = 208/417 (49%), Gaps = 25/417 (5%)

Query: 16  EYEQEYSAHNY----HPLPVV-FSRASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHIIQ 70
           ++++E+  H Y     PLPV    RA GA +   +G+  ++ +S++     G+ HP + Q
Sbjct: 386 QFDREHLWHPYTSTTDPLPVYKVKRADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQ 445

Query: 71  ALVDQASKLT-LSSRAFSNDCFASFSKFVTEFF--GYESVLPMNTGAEAVESALKLARRW 127
           A  DQ  K++ +     ++D      K +        + +   ++G+ AVE ALK+A ++
Sbjct: 446 AAKDQLDKMSHVMFGGLTHDPAIELGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQY 505

Query: 128 GYMVKKIQPNEAIILGARGNFHGRTFGAISLSTDEEDSRMNFGPFLE-NVTAKIPGGSDD 186
            Y   K   N  + +  R  +HG T+ A+S+          FG  L        P    D
Sbjct: 506 WYAAGKPDKNNFVTI--RSGYHGDTWNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFD 563

Query: 187 EFIRYGEIDDYKRAFESHGDKICAVIVEPI-QGEAGIVVPRADFLTDLQELCKKHQVLLI 245
                 EI   +   E H  ++ A+I+EPI QG  G+      +L + ++LCK+H +LLI
Sbjct: 564 GEWNPDEIIPLRETIEKHSKELAALILEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLI 623

Query: 246 CDEIQTGIARTGKLLCYEHSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGS-- 303
            DEI TG  RTGKL  +EH+   +PDI+ +GKA++GG + +S VL+S +I D  +  +  
Sbjct: 624 FDEIATGFGRTGKLFAWEHA-GVEPDIMCIGKALTGGYMTLSAVLASNQIADTISNHAPK 682

Query: 304 ---HGSTYGGNPLASRVAIAALEVVQNENLVERSARLGKFLQDELVKLQHESNGVISEVR 360
              HG T+ GNPLA  VA A++ ++ +    E   R+   L++EL   +      +++VR
Sbjct: 683 AFMHGPTFMGNPLACAVACASVRLLLDSGWAENVKRIEAQLKEELAPARKFPQ--VADVR 740

Query: 361 GKGLLTAIVINPEKANGRTAWDLCLLMKDQGVLAKPTHEHIIRLAPPLVISEEDLLK 417
             G +   VI  E++          +  ++G+  +P  + ++ L PP +IS E L K
Sbjct: 741 ILGAIG--VIQTERSVSMAYMQRRFV--EEGIWVRPFGK-LVYLMPPFIISPEQLSK 792


Lambda     K      H
   0.318    0.136    0.400 

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: 732
Number of extensions: 43
Number of successful extensions: 6
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: 437
Length of database: 804
Length adjustment: 37
Effective length of query: 400
Effective length of database: 767
Effective search space:   306800
Effective search space used:   306800
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