GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pseudomonas simiae WCS417

Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate GFF3098 PS417_15850 alcohol dehydrogenase

Query= SwissProt::Q0KDL6
         (366 letters)



>FitnessBrowser__WCS417:GFF3098
          Length = 357

 Score =  516 bits (1329), Expect = e-151
 Identities = 260/363 (71%), Positives = 296/363 (81%), Gaps = 7/363 (1%)

Query: 3   AMMKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTVGH 62
           A MKAA+FVE  RI L DKPIP++GP DAL+RITTTTICGTDVHIL+GEYPVAKGLT+GH
Sbjct: 2   ATMKAAIFVEKNRIVLEDKPIPEVGPLDALIRITTTTICGTDVHILRGEYPVAKGLTIGH 61

Query: 63  EPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHGYK 122
           EPVGIIE+LGS V G+ EGQRVIAGAI P+  SYA   G ASQDG           HG++
Sbjct: 62  EPVGIIERLGSQVRGFVEGQRVIAGAITPSGQSYACLCGCASQDGPDTR-------HGFR 114

Query: 123 ATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENANIR 182
           AT GW+FGN+IDG QAEYVLVPDA ANL PIPDGL+DEQVLMCPDIMSTGF GAE   I 
Sbjct: 115 ATGGWKFGNIIDGCQAEYVLVPDALANLCPIPDGLSDEQVLMCPDIMSTGFSGAERGEIN 174

Query: 183 IGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDVVD 242
           IGDTVAVFA GPIGLCA AGARL GATTII +D    R+ +AR++GA  V+NF+  +VV+
Sbjct: 175 IGDTVAVFALGPIGLCAVAGARLKGATTIIGVDAVAQRMSVARQLGATHVVNFKEANVVE 234

Query: 243 EVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGLGD 302
           ++M LT GRGVD SIEALGTQ TFE +LRVL+PGG LSSLGVYSSDL IPL AFAAGLGD
Sbjct: 235 QIMALTDGRGVDVSIEALGTQGTFESALRVLRPGGRLSSLGVYSSDLRIPLDAFAAGLGD 294

Query: 303 HKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLKIA 362
           + I T LCPGGKERMRRL+ V++SG VDL  LVTH ++LDDI AAY+LFANQRDGV+K+A
Sbjct: 295 YSIVTTLCPGGKERMRRLMAVVQSGAVDLSPLVTHHFKLDDIEAAYELFANQRDGVMKVA 354

Query: 363 IKP 365
           I P
Sbjct: 355 ITP 357


Lambda     K      H
   0.320    0.138    0.408 

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: 547
Number of extensions: 19
Number of successful extensions: 2
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: 366
Length of database: 357
Length adjustment: 29
Effective length of query: 337
Effective length of database: 328
Effective search space:   110536
Effective search space used:   110536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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:

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