GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Pseudomonas fluorescens FW300-N1B4

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate Pf1N1B4_4502 Aldehyde dehydrogenase (EC 1.2.1.3)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4502 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 506

 Score =  932 bits (2410), Expect = 0.0
 Identities = 452/506 (89%), Positives = 479/506 (94%)

Query: 1   MIYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEK 60
           MIYAQPGTPGAV+SFKPRYGN+IGGEFV P+ GEYF NTSPV GEVIAEFPRS A DIEK
Sbjct: 1   MIYAQPGTPGAVISFKPRYGNFIGGEFVAPINGEYFTNTSPVTGEVIAEFPRSSAADIEK 60

Query: 61  ALDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPL 120
           ALDAAHAAADAWGKTS QDR+L+LLKIADRIE NLE LAV ETWDNGKAVRETLNADVPL
Sbjct: 61  ALDAAHAAADAWGKTSAQDRSLVLLKIADRIEQNLEILAVTETWDNGKAVRETLNADVPL 120

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

Query: 181 AGNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTG 240
           AGNCIVLKPAEQTPLSIMVF E++ DLLP GVLNIVQGFGREAG+ALATS RIAKIAFTG
Sbjct: 181 AGNCIVLKPAEQTPLSIMVFAELIADLLPAGVLNIVQGFGREAGEALATSKRIAKIAFTG 240

Query: 241 STPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEV 300
           STP+G+HIM CAAENIIPSTVELGGKSPNIFFEDIMNAEP FIEKAAEGLVLAFFNQGEV
Sbjct: 241 STPIGAHIMHCAAENIIPSTVELGGKSPNIFFEDIMNAEPQFIEKAAEGLVLAFFNQGEV 300

Query: 301 CTCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQ 360
           CTCPSRAL+QESI+EPFM  VMKKI  IKRGNPLDT+TMVGAQASEQQ+DKILSY++IAQ
Sbjct: 301 CTCPSRALVQESIYEPFMAEVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQ 360

Query: 361 QEGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEAL 420
           +EGA++LTGGAAE+LEG LS+GYY+QPTL+KGHNKMRVFQEEIFGPVVG+ TFKDEAEAL
Sbjct: 361 EEGAELLTGGAAERLEGDLSSGYYIQPTLLKGHNKMRVFQEEIFGPVVGITTFKDEAEAL 420

Query: 421 AIANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480
           AIAND+EFGLGAG+WTRDINRAYRMGR IKAGRVWTNCYHLYPAHAAFGGYKKSGVGRE 
Sbjct: 421 AIANDSEFGLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGREN 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: 883
Number of extensions: 30
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 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, 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