GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Geobacter daltonii FRC-32

Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_012648616.1 GEOB_RS17645 aldehyde dehydrogenase

Query= CharProtDB::CH_007936
         (497 letters)



>NCBI__GCF_000022265.1:WP_012648616.1
          Length = 475

 Score =  302 bits (774), Expect = 1e-86
 Identities = 175/473 (36%), Positives = 272/473 (57%), Gaps = 14/473 (2%)

Query: 21  LFINNEFVKGVEGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFEGPWRQVTPSE 80
           + I+ E++ G +    +VINP ++ +I  V EAT +DV+ A+ AA   FE     +   +
Sbjct: 7   MLIDGEWL-GDDRSGIEVINPFDDSLIGLVPEATAEDVEAAIIAAAKGFERI-SAMPAHK 64

Query: 81  RGILINKLADLMERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQTI 140
           R  ++ K A+L+ RD D +A I + + GK++  A  +   S    ++ A  A   HG+ +
Sbjct: 65  RSDILEKTAELILRDKDEIAGIIAREAGKSWKYAVAEAERSAETFKFAAIEAKASHGEIV 124

Query: 141 DTNPETLTYTR-----HEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPL 195
             +   ++  R       P+G+ G I P+NFPL + + K+ PA+A GN VVLK A +TPL
Sbjct: 125 PMDASAVSAGRFGFYIRTPIGIIGAITPFNFPLNLVAHKLAPAIATGNAVVLKPATKTPL 184

Query: 196 SALYAAKLIKEAGFPAGVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAK 255
           ++L  A+L+ EAG PAG +NV+ G G T G  +     +  + FTGS  VGR I    ++
Sbjct: 185 TSLKLAELLMEAGLPAGALNVLIGSGSTVGNRLVEDNRLAMITFTGSPPVGRGI---KSR 241

Query: 256 SNLKKVTLELGGKSPNIVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFV 315
           S LK+VTLELG  SP I+ +D D+D A+S    G F N GQ C +  RI V +  YD+F+
Sbjct: 242 SGLKRVTLELGSNSPTIIEEDGDVDKAVSRCVVGSFANSGQVCISVQRIFVHKDRYDEFI 301

Query: 316 ARFKERAQKNKVGNPFEQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGNEGY 375
           A+F E     KVG+PF++ +  GP ++  + +R +E++   K  GA VA GG+  GN   
Sbjct: 302 AKFVEATCALKVGDPFDKSSDIGPMITTKELNRALEWLEEAKNLGAVVAAGGNAIGN--- 358

Query: 376 FIQPTVFTDVTSDMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTA 435
            ++PT+ T VT +MK+   E+F P+V++  +    EA+++ + + YGL A ++T+++N A
Sbjct: 359 CLEPTILTGVTREMKVMCSEVFAPIVSVLPYDTFDEALEMADDSVYGLQAGIYTRDINKA 418

Query: 436 IRVSNALKAGTVWINNYNMISY-QAPFGGFKQSGLGRELGSYALENYTQIKTV 487
            +    L  G V IN+         P+GG K+SGLGRE   YA+E  T IK V
Sbjct: 419 FKAIKKLDVGGVIINDVPTFRVDHMPYGGNKESGLGREGLKYAMEEMTNIKMV 471


Lambda     K      H
   0.318    0.134    0.397 

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: 556
Number of extensions: 16
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: 497
Length of database: 475
Length adjustment: 34
Effective length of query: 463
Effective length of database: 441
Effective search space:   204183
Effective search space used:   204183
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