GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Shewanella loihica PV-4

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate 5208068 Shew_0580 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-12387
         (496 letters)



>FitnessBrowser__PV4:5208068
          Length = 487

 Score =  171 bits (434), Expect = 4e-47
 Identities = 139/428 (32%), Positives = 204/428 (47%), Gaps = 24/428 (5%)

Query: 52  TPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEA 111
           TPE V+ AVEAA  A   W       R A+V+ + + L  HK D+A+++  E GK + E 
Sbjct: 36  TPEQVNAAVEAARAAQFDWFMLGFDARLAIVEAYRDQLEAHKGDIAEVIAQETGKPQWET 95

Query: 112 LGEVQEMIDICDFAVGLSRQLYGR---TMPSERPGHRLMETWHPLGVVGVISAFNFPVAV 168
             E   MI      +GLS   Y +   T  ++ P  R +    P GVV V   +NFP  +
Sbjct: 96  ATEAGAMIG----KIGLSVAAYHKRTGTSENDTPAGRAVLRHKPHGVVAVFGPYNFPGHL 151

Query: 169 WAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGER 228
              +   AL+ G+TVV+KPSELTP      A L+      AG P G+  +V G  + G+ 
Sbjct: 152 PNGHIVPALLAGNTVVFKPSELTP----KTAELMLKLWEKAGLPAGVINLVQGEVETGKA 207

Query: 229 LVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTI-LELGGNNAAVVTPSADLDLTVNAAV 287
           L   P++  +  TGS+R G  +  + A   G+ + LE+GGNN  ++    D    V+  +
Sbjct: 208 LASHPQIDGLFFTGSSRTGHILHQQYAGHPGKILALEMGGNNPLIIKGVKDTLAAVHDII 267

Query: 288 FAAAGTAGQRCTTLRRLIVHEDI-ADTVVERLTAAFERLPIGD-PFQDTTLVGPLVNEAA 345
            +A  ++GQRCT  RRL V +    D ++ +L  A +++ +G    Q    +G +++EAA
Sbjct: 268 QSAYISSGQRCTCARRLYVEKGAEGDALLAKLAEAVKQIKVGPWNAQPQPFMGSMISEAA 327

Query: 346 FGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPILY 405
              M EA       GGT       +      G   V P L+ +     +  EE F P+L 
Sbjct: 328 AKGMVEAQRNLINLGGTPLV----ELKHLEAGTGLVSPGLIDVTQVIELPDEEYFGPLLQ 383

Query: 406 VLTYRDLDEAIRLNNEVPQACRQGSRTDGAPADDPRCRARRRAGGANC-PAVPGRSGT-- 462
           V+ Y D DEAI+L N+       G   D +  D     AR RAG  N    + G SG+  
Sbjct: 384 VVRYTDFDEAIKLANDTRYGLSAGILAD-SREDYDYFLARIRAGIVNWNKQITGASGSAP 442

Query: 463 --GAGAGG 468
             G GA G
Sbjct: 443 FGGVGASG 450


Lambda     K      H
   0.320    0.135    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: 492
Number of extensions: 23
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: 496
Length of database: 487
Length adjustment: 34
Effective length of query: 462
Effective length of database: 453
Effective search space:   209286
Effective search space used:   209286
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 (21.8 bits)
S2: 52 (24.6 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