GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Pseudomonas fluorescens FW300-N2E2

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate Pf6N2E2_1381 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::psRCH2:GFF2231
         (506 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1381 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 506

 Score =  947 bits (2448), Expect = 0.0
 Identities = 463/506 (91%), Positives = 484/506 (95%)

Query: 1   MIYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEK 60
           MIYAQPGTPGAVVSFKPRYGN+IGGEFV PV GEYF NTSPVNGEVIAEFPRS A DI+K
Sbjct: 1   MIYAQPGTPGAVVSFKPRYGNFIGGEFVAPVNGEYFTNTSPVNGEVIAEFPRSSAADIDK 60

Query: 61  ALDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPL 120
           ALDAAHAAADAWGKTSVQDR+L+LLKIADRIE NLE LAV+ETWDNGKAVRETLNADVPL
Sbjct: 61  ALDAAHAAADAWGKTSVQDRSLVLLKIADRIEQNLEILAVSETWDNGKAVRETLNADVPL 120

Query: 121 AADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180
           AADHFRYFAGCIRAQEG AAEINE T AYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA
Sbjct: 121 AADHFRYFAGCIRAQEGGAAEINELTTAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180

Query: 181 AGNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTG 240
           AGNCIVLKPAEQTPLSIMVFIE+V DLLPPGVLNIV GFGREAG+ALATS RIAKIAFTG
Sbjct: 181 AGNCIVLKPAEQTPLSIMVFIELVADLLPPGVLNIVHGFGREAGEALATSKRIAKIAFTG 240

Query: 241 STPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEV 300
           STP+GSHIM+CAAENIIPSTVELGGKSPNIFFEDIM AEPAFIEKAAEGLVLAFFNQGEV
Sbjct: 241 STPIGSHIMKCAAENIIPSTVELGGKSPNIFFEDIMQAEPAFIEKAAEGLVLAFFNQGEV 300

Query: 301 CTCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQ 360
           CTCPSRAL+QESI+ PFM  VMKKI  IKRGNPLDT+TMVGAQASEQQFDKILSY+EIAQ
Sbjct: 301 CTCPSRALVQESIYAPFMAEVMKKIAKIKRGNPLDTETMVGAQASEQQFDKILSYLEIAQ 360

Query: 361 QEGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEAL 420
           QEGA++LTGGAAE+LEG LS+GYY+QPTL+KGHNKMRVFQEEIFGPVVGV TFKDEAEAL
Sbjct: 361 QEGAELLTGGAAERLEGDLSSGYYIQPTLLKGHNKMRVFQEEIFGPVVGVTTFKDEAEAL 420

Query: 421 AIANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480
           AIANDTEFGLGAG+WTRDINRAYRMGR IKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET
Sbjct: 421 AIANDTEFGLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480

Query: 481 HKMMLDHYQQTKNLLISYDINPLGFF 506
           HKMMLDHYQQTKNLL+SYDINPLGFF
Sbjct: 481 HKMMLDHYQQTKNLLVSYDINPLGFF 506


Lambda     K      H
   0.319    0.136    0.406 

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: 898
Number of extensions: 29
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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: 52 (24.6 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