GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Pseudarthrobacter sulfonivorans Ar51

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase

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



>NCBI__GCF_001484605.1:WP_058929223.1
          Length = 508

 Score =  214 bits (546), Expect = 4e-60
 Identities = 134/387 (34%), Positives = 198/387 (51%), Gaps = 9/387 (2%)

Query: 39  PLTGADLFGLRAHTPEDVDRAVEAAHTAFLT--WRTTPAPVRGALVKRFGELLTEHKQDL 96
           P   A    + A T EDVDRAV AA  AF    W  T    R AL++RF +LLTE+  +L
Sbjct: 43  PYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQTLPSQRAALLRRFADLLTENADEL 102

Query: 97  ADLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVV 156
           A     E GK+  E      +M     +  GL+  + GRT+ S  P         P+GVV
Sbjct: 103 ARGQIHENGKLIGEMTWGALQMGQHAHYVAGLAETIQGRTIESNWPNTAAFTFREPIGVV 162

Query: 157 GVISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLN 216
            +I+ +N P+ + +W    AL  G+TVV KPSE TP +    A L      +AG P G+ 
Sbjct: 163 AMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATPTSTLRMAELA----MEAGFPPGVI 218

Query: 217 QVVVGAAD-VGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTP 275
            VV G     G  LVD   V  ++ TGST  GRA+  + A RF R  LELGG +  ++  
Sbjct: 219 NVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQAAERFARVTLELGGKSPNIIFS 278

Query: 276 SADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTT 335
            AD+D  V+ A+    G  GQ C    R++V + I D  V+R+  A + L +GDP   T 
Sbjct: 279 DADIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFVDRMARATQALTLGDPLDPTV 338

Query: 336 LVGPLVNEAAFGRMREAVERATAEGGTLCAGGER--QFPDAAPGAYYVRPALVRMPAQTA 393
            +GP+ N A F ++ + V+   +EG  + AGG R     + + G ++       +  ++ 
Sbjct: 339 DMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSELSKGLFFEPTVFANVSNESR 398

Query: 394 VVREETFAPILYVLTYRDLDEAIRLNN 420
           + +EE F P+  ++ +RD DEA+++ N
Sbjct: 399 LAQEEIFGPVASIIRFRDEDEAVKIAN 425


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: 493
Number of extensions: 27
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: 508
Length adjustment: 34
Effective length of query: 462
Effective length of database: 474
Effective search space:   218988
Effective search space used:   218988
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 Apr 09 2024. 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