GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:350970
          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:

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