GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucO in Desulfovibrio vulgaris Hildenborough

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 208042 DVU2545 alcohol dehydrogenase, iron-containing

Query= metacyc::STM4044-MONOMER
         (382 letters)



>lcl|MicrobesOnline__882:208042 DVU2545 alcohol dehydrogenase,
           iron-containing
          Length = 386

 Score =  265 bits (678), Expect = 1e-75
 Identities = 147/369 (39%), Positives = 209/369 (56%)

Query: 14  GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73
           G GA       V N    + L+VTD  +++ G  D++  +L  + +++ +F ++ PNP +
Sbjct: 18  GNGAARLAGRYVHNLGGTRCLVVTDPGVMRNGHADTVIGSLTAYGIAHAVFQDISPNPRD 77

Query: 74  ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLV 133
             VQ+G  AY    CD I+A GGGSPID AK + I+ +N G  + Y GV  +     PLV
Sbjct: 78  VEVQRGVEAYHREGCDAIVAVGGGSPIDCAKGIGIVASNGGSISLYEGVDAIPKPMPPLV 137

Query: 134 AINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMD 193
            + TTAG+AA+++  A+I D+ R VK  I+    + D+++ D S    +   +TAATG+D
Sbjct: 138 CVPTTAGSAADVSQFAIITDTTRMVKIAIVSKAAVADVSLIDPSTTKSMSRDLTAATGID 197

Query: 194 ALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAF 253
            LTHA+EA+ S  + P+TD  ALEAI L+N  LP+ + DG +  ARE MA     AG+AF
Sbjct: 198 TLTHAIEAFASNASGPITDMFALEAISLVNTHLPQVLADGDDDTAREGMALACLNAGLAF 257

Query: 254 NSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETRGM 313
           ++A LG VHA+AH  G   +LPHG CNAILLP V   N   A  R+AR+A A+G++  G 
Sbjct: 258 SNAILGAVHAMAHSLGGLLDLPHGECNAILLPFVVRRNFDAAPVRYARVANALGIDVGGT 317

Query: 314 SDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRDE 373
              A      + + TL    G   G S  GVT+E I      A+ DPC   NP      +
Sbjct: 318 PATAIRDALFDRLMTLRTAAGFTRGLSAFGVTREQIGRLARLAVEDPCLATNPEALDIAD 377

Query: 374 VRGLYLEAL 382
           +  LY EAL
Sbjct: 378 IESLYAEAL 386


Lambda     K      H
   0.317    0.133    0.384 

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: 443
Number of extensions: 13
Number of successful extensions: 1
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: 382
Length of database: 386
Length adjustment: 30
Effective length of query: 352
Effective length of database: 356
Effective search space:   125312
Effective search space used:   125312
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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