GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Microvirga lotononidis WSM3557

Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_040639379.1 MICLODRAFT_RS25285 aldehyde dehydrogenase family protein

Query= CharProtDB::CH_007936
         (497 letters)



>NCBI__GCF_000262405.1:WP_040639379.1
          Length = 478

 Score =  339 bits (869), Expect = 1e-97
 Identities = 188/461 (40%), Positives = 266/461 (57%), Gaps = 8/461 (1%)

Query: 32  EGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFEGPWRQVTPSERGILINKLADL 91
           +G T  V++P +  ++  +   T +D+D AV AARAAFEG W ++T +ERG L+ KLA  
Sbjct: 16  DGMTLDVLSPVDGSLLARIAAGTTQDIDEAVKAARAAFEGAWGELTATERGRLLMKLATA 75

Query: 92  MERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQTIDTNPETLTYTR 151
           +E   D LA +ES DNGK    ++ D         +Y   ADK+HG  I           
Sbjct: 76  VEARADELAILESRDNGKPLRQSRADAIALARYFEFYGSAADKLHGDVIPYLNTHFIGVE 135

Query: 152 HEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSALYAAKLIKEAGFPA 211
             P GV G I+PWN+P+ ++   +G A+AAGN  V+K AE   L+ L  + L +E GFP 
Sbjct: 136 RVPHGVTGHIVPWNYPMQIFGRSVGAALAAGNATVVKPAEDASLTILRVSALAREVGFPD 195

Query: 212 GVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSNLKKVTLELGGKSPN 271
           G +NV++G GRTAGAA+++H  ID ++FTGS   G T +Q AA  N   VTLELGGKS  
Sbjct: 196 GALNVVTGLGRTAGAALAAHSGIDFLSFTGSPETG-TAVQTAAARNHVGVTLELGGKSAQ 254

Query: 272 IVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVARFKERAQKNKVGNPF 331
           +VFDDAD++ A+      I  N GQ C AGSR+L+Q GI+   V    ER +  + G+P 
Sbjct: 255 VVFDDADLERALPTLVNAIIQNGGQTCSAGSRLLIQRGIFQDVVDAVAERFRTLRAGHP- 313

Query: 332 EQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGG----DRHGNEGYFIQPTVFTDVTS 387
           E +   GP ++Q Q  R++ Y+  G+  G  V   G    D     GY++ P     V  
Sbjct: 314 EHEPDLGPMINQAQQRRVLGYLERGRNEGLNVVGEGVVALDAPAG-GYYVAPAFLAPVPH 372

Query: 388 DMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTAIRVSNALKAGTV 447
           +  ++QEE+FGPV+    F DEAEA ++ N T YGLAA V T++   + RV+ +++AG V
Sbjct: 373 ESILSQEEVFGPVLVATPFDDEAEATRLANGTPYGLAAGVWTRDAMRSTRVARSIRAGQV 432

Query: 448 WINNYNM-ISYQAPFGGFKQSGLGRELGSYALENYTQIKTV 487
           ++N Y      + PFGGF +SG GRE G   L  +T  KT+
Sbjct: 433 FVNCYGAGGGIELPFGGFGRSGHGREKGFEGLVEFTTTKTL 473


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: 518
Number of extensions: 26
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: 478
Length adjustment: 34
Effective length of query: 463
Effective length of database: 444
Effective search space:   205572
Effective search space used:   205572
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