GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Pseudomonas simiae WCS417

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate GFF2557 PS417_13035 aldehyde dehydrogenase

Query= metacyc::MONOMER-12746
         (434 letters)



>FitnessBrowser__WCS417:GFF2557
          Length = 1175

 Score =  226 bits (576), Expect = 3e-63
 Identities = 151/389 (38%), Positives = 207/389 (53%), Gaps = 36/389 (9%)

Query: 25   QALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPD-KTGIGDYSFE 83
            +A +++G  LA  GDC  CHTA  G   AGGL M+TP G +YS+NITPD KTGIG +S+ 
Sbjct: 794  KATLERGRLLAAVGDCAVCHTAPGGATNAGGLAMQTPFGTLYSSNITPDVKTGIGAWSYP 853

Query: 84   DFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDNQDSDIPWP 143
             F++A+R G+ + G  LYPA P+ ++  +++ADMQALYAY M  V PV      S  P P
Sbjct: 854  AFERAMRDGIGRDGRNLYPAFPYTAFRNINEADMQALYAYLMSQV-PV------SQAPTP 906

Query: 144  LSMRWPLSI------WRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHTPRALT 197
             +MR+P +I      W  +     E  +P        +RG YLV GLGHC ACH+PR L 
Sbjct: 907  NAMRFPFNIRPLMAGWNALNLRRGEI-SPQPERSEQWNRGNYLVNGLGHCAACHSPRNLM 965

Query: 198  MQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVF 257
              EK     GG  FL+G   ++GW A +L G  K     W+E+QL  +L TG SD   V 
Sbjct: 966  GAEK-----GGKSFLAGGT-VDGWEAPALNGLSKAST-PWTEDQLFTYLSTGYSDAHGVA 1018

Query: 258  GGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDDSKPGAA 317
             G    VV  +  +  AD+ A+A YL SL  +   + P       A  + N D    G  
Sbjct: 1019 AGPMGPVVSELSKLPKADIRAMAVYLASLKGDAAAEAP----AVTAANVPNPD----GRR 1070

Query: 318  VYIDNCAACHRTDGHG--YTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTF 375
            V+   C ACH  DG G     V P+ A N  + S    +LI ++L+G + PAT       
Sbjct: 1071 VFEGACKACH-ADGLGPKLFGVSPSFATNTNVHSDQPDNLIKVILQGISKPATQDLG--- 1126

Query: 376  TMPAFAWRLSDQEVADVVNFIRSSWGNQA 404
             MP F   LS+ +VAD+  ++R+ +   A
Sbjct: 1127 YMPGFKDSLSNSQVADLAAYLRAQFAPNA 1155


Lambda     K      H
   0.316    0.131    0.404 

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: 1414
Number of extensions: 93
Number of successful extensions: 8
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: 434
Length of database: 1175
Length adjustment: 39
Effective length of query: 395
Effective length of database: 1136
Effective search space:   448720
Effective search space used:   448720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 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