GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF3098 PS417_15850 alcohol
           dehydrogenase
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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