GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Microvirga lotononidis WSM3557

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_009763662.1 MICLODRAFT_RS20175 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_000262405.1:WP_009763662.1
          Length = 495

 Score =  521 bits (1342), Expect = e-152
 Identities = 259/480 (53%), Positives = 346/480 (72%), Gaps = 6/480 (1%)

Query: 46  LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LL G ++V G W+  P   T PV DP  GA +  V D G   AR A+  A+     W + 
Sbjct: 20  LLVGQAYVAGEWIDAPDGKTIPVTDPFDGALILEVPDLGPDAARRAIDKAHAVQKDWAKR 79

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KERS++LR+WYDL++ N D+LA I+T E GKPL EA+GE++ +A ++EWF+EEA+R+ 
Sbjct: 80  TAKERSAILRRWYDLIVANADDLALILTTEQGKPLAEAKGEVISNAAYIEWFAEEAKRID 139

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD+I  +   +R +VLKQPVGV + ITPWNFP+ MITRKVG ALAAGCT+V+KPA  TP 
Sbjct: 140 GDVIPGATPSQRIVVLKQPVGVCAAITPWNFPNGMITRKVGPALAAGCTMVLKPAAQTPL 199

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA LA +AG+P G ++V+     +AK +GE  C +P V+KI+FTGST  G+ L+  
Sbjct: 200 SALALAVLAERAGVPKGAFSVV---TGEAKPIGEEFCHNPKVAKITFTGSTGVGRWLMKE 256

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
           AA+ +KR+S+ELGG APFIVFD A++D AV GAMASKFRNAGQTCVC+NR  VQ G+ ++
Sbjct: 257 AADGIKRLSLELGGNAPFIVFDDADLDAAVEGAMASKFRNAGQTCVCANRIYVQEGVAEA 316

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K A A   SL++G G + G T GPLI+++AV K+E+HV D + KG  ++ GGKR   
Sbjct: 317 FAEKLA-AKAGSLKLGRGTDAGVTMGPLIDDRAVAKMEEHVRDVLDKGGKLLVGGKRSDL 375

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           G  FFEPT+++ VT+ M    EETF P+AP+I F  E + +A+AN ++ GLA YFY++D 
Sbjct: 376 GSTFFEPTVMTGVTQAMKVTKEETFAPLAPIITFKDEADVIAMANDSEFGLASYFYAKDM 435

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
           A++WRVAE LE GMVGVN   +++   PFGGVKQSGLGREGSKYGI+ +LE+KY+   GL
Sbjct: 436 ARVWRVAEALESGMVGVNTPALANEMAPFGGVKQSGLGREGSKYGIEGFLEIKYINLAGL 495


Lambda     K      H
   0.318    0.135    0.400 

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: 678
Number of extensions: 25
Number of successful extensions: 3
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: 523
Length of database: 495
Length adjustment: 34
Effective length of query: 489
Effective length of database: 461
Effective search space:   225429
Effective search space used:   225429
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