GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Streptomyces kebangsaanensis SUK12

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  223 bits (569), Expect = 9e-63
 Identities = 153/458 (33%), Positives = 225/458 (49%), Gaps = 15/458 (3%)

Query: 21  YPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHK 80
           + V  P  G ++ + +L G  +  A +  A+ AF  W       R + +  F EVL +  
Sbjct: 38  HAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRA 97

Query: 81  ADLGELVSIEAGK---ITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETW 137
            D     S++ GK   +T+E   +V   ID   F  G +R L G +       H      
Sbjct: 98  EDFARAESLQCGKPLKLTREF--DVPGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRR 155

Query: 138 HPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFG 197
            P+GVVG I+ +N+P+ + AW    A+ AGN++V KP+E TPLT+L    LF +A    G
Sbjct: 156 EPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSL----LFAQAATEAG 211

Query: 198 DAPAGLAQLVIG-GREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGN 256
             P G+  +V G G+EAGE +V  P V +VS TGST +G+ V     A   R  LELGG 
Sbjct: 212 -IPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLELGGK 270

Query: 257 NAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIG 316
              ++   ADL+ AV G +  A+   GQ CT   R  V R + +E VAR  A    VR+G
Sbjct: 271 APFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLG 330

Query: 317 DPRKDNL-VGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAIAEMP 375
           DP      +GPLI     D + G + +AR     V GGE    +    AYY    IA   
Sbjct: 331 DPFAPGTDLGPLISHVHRDRVAGFVDRARAYARVVTGGEAPQGELKNGAYYRPTLIAGAA 390

Query: 376 AQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDC 435
             S++V+ E F P+L VL +D  +E +RL N+   GL++  ++ D+  A R      + C
Sbjct: 391 QDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGC 450

Query: 436 GIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGY 473
              N +I           GG K++G G++  S +++ Y
Sbjct: 451 VWVNDHIPIISEM---PHGGSKQSGFGKDMSSYSFEEY 485


Lambda     K      H
   0.318    0.135    0.396 

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: 610
Number of extensions: 32
Number of successful extensions: 4
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: 511
Length adjustment: 34
Effective length of query: 462
Effective length of database: 477
Effective search space:   220374
Effective search space used:   220374
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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