GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Luteipulveratus mongoliensis MN07-A0370

Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_052594900.1 VV02_RS21400 aldehyde dehydrogenase family protein

Query= CharProtDB::CH_007936
         (497 letters)



>NCBI__GCF_001190945.1:WP_052594900.1
          Length = 494

 Score =  372 bits (955), Expect = e-107
 Identities = 193/473 (40%), Positives = 294/473 (62%), Gaps = 7/473 (1%)

Query: 21  LFINNEFVKGVEGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFE-GPWRQVTPS 79
           L+I  ++V   +G T ++ NP+N +V   V EAT  D   AVAAAR+AF+ G W     +
Sbjct: 8   LYIAGDWVHSSDGGTRELTNPANGEVFAVVDEATPADATRAVAAARSAFDQGDWPATPVN 67

Query: 80  ERGILINKLADLMERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQT 139
           ER  L++++ADL+ERD + LA IE+ D GK    +++D+ + +   RYY+        + 
Sbjct: 68  ERAALLDRIADLLERDKEALARIETEDTGKTLVESRIDIDDVVSVFRYYSRLVGIESDRL 127

Query: 140 IDT-NPETLTYTRHEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSAL 198
           +D  +P+ ++    EP+GVC  I PWN+PLL  SWK+ PA+AAG T+V K +E TPLS +
Sbjct: 128 VDVGDPDVMSTVVREPIGVCVLIAPWNYPLLQMSWKVAPALAAGCTMVAKPSEVTPLSTI 187

Query: 199 YAAKLIKEAGFPAGVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSNL 258
              +LI+EAG PAGV+N++ G G T GAA++   D+D ++FTG    GR + +AAA+  +
Sbjct: 188 AFVRLIEEAGAPAGVVNLVQGSGATLGAALTETPDVDLISFTGGLATGRIVAKAAAQ-QV 246

Query: 259 KKVTLELGGKSPNIVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVARF 318
            +  +ELGGK+P+IVF D + ++++     G+F + GQ C AG+R++++E I D FVA  
Sbjct: 247 TRCAVELGGKNPHIVFADTEWESSVDQVLTGVFLHSGQVCSAGTRLIIEESIADDFVAAL 306

Query: 319 KERAQKNKVGNPFEQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGN----EG 374
             RA   ++G+  +  +  GP VSQ    ++  Y+  G   GAT+ TGG R  +    +G
Sbjct: 307 AARAATIRMGDGLDPASETGPLVSQDHLAKVEAYVALGISEGATLVTGGSRPTDPSLAKG 366

Query: 375 YFIQPTVFTDVTSDMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNT 434
            F  PT+       M+I QEE FGP++T+++F  E EAI++GN T+YGLAA V T +   
Sbjct: 367 SFYLPTILDRCDRTMRIVQEETFGPILTVERFTTEEEAIRLGNDTEYGLAAGVRTSDPGR 426

Query: 435 AIRVSNALKAGTVWINNYNMISYQAPFGGFKQSGLGRELGSYALENYTQIKTV 487
             RV+ AL+ GTVW+N++   +  A +GGFK+SG GRELG   L  Y ++K +
Sbjct: 427 GERVARALRHGTVWLNDFGYYTAAAEWGGFKKSGNGRELGPAGLAEYQELKHI 479


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: 520
Number of extensions: 17
Number of successful extensions: 5
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: 494
Length adjustment: 34
Effective length of query: 463
Effective length of database: 460
Effective search space:   212980
Effective search space used:   212980
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