GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4502
          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 (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