GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Amycolatopsis halophila YIM 93223

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= uniprot:Q88CC3
         (496 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  207 bits (528), Expect = 5e-58
 Identities = 148/460 (32%), Positives = 228/460 (49%), Gaps = 20/460 (4%)

Query: 23  VHTPIDGSQIASVKLLGKAETIARIDQAQSAFE--AWRSVPAPRRGELVRLFGEVLREHK 80
           V  P + +++A+V    + +  A +  A+ AF+   WR+  A  RGEL+R    +L+  K
Sbjct: 22  VLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTARERGELLREIARLLQRDK 81

Query: 81  ADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPL 140
             L    S++ GK   EG  +V ++  +  +   L+    G  + +       R    P+
Sbjct: 82  EHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAGRVVDTGDASVISRVVHEPV 141

Query: 141 GVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAP 200
           GV  +I+ +N+P+   +W  A AL AGN+VV KPSE TPLT +    L E+A       P
Sbjct: 142 GVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLTTIELMRLVEEA-----GVP 196

Query: 201 AGLAQLVI-GGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAM 259
           AG+  LV+ GG   G  MV  P V LVS TG    G+++    A    R  LELGG N  
Sbjct: 197 AGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEGVKRVALELGGKNPN 256

Query: 260 ILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIG--- 316
           ++   AD D AV   L +A   +GQ C+   RLIV   I DE VA +      +R+G   
Sbjct: 257 VVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAELARRADAIRLGDGL 316

Query: 317 DPRKDNLVGPLIDKQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAI-AEM 374
           DP  +   GPL   +  D ++  + +A+ EG + V GG R    +  + Y++ P + A+ 
Sbjct: 317 DPATE--CGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELADGYFLRPTVFADC 374

Query: 375 PAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSA-SGS 433
             +  +V+ E F P++ V  +D  +EA+RL N+   GL+  ++T+D   A+R   A    
Sbjct: 375 DREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDASRAQRVAGALRHG 434

Query: 434 DCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGY 473
              I + +     AE GG FG   ++G GRE G    + Y
Sbjct: 435 TVWINDFHPYLPQAEWGG-FG---KSGIGRELGPSGLEEY 470


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: 571
Number of extensions: 28
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 496
Length adjustment: 34
Effective length of query: 462
Effective length of database: 462
Effective search space:   213444
Effective search space used:   213444
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