GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Pseudomonas putida KT2440

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate PP_2185 PP_2185 putative Formate dehydrogenase, alpha subunit

Query= uniprot:Q39TW6
         (218 letters)



>FitnessBrowser__Putida:PP_2185
          Length = 960

 Score =  104 bits (259), Expect = 7e-27
 Identities = 71/240 (29%), Positives = 111/240 (46%), Gaps = 40/240 (16%)

Query: 3   EINLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVE-VRGWPK 61
           +++L IDG+ +    G +++ AA  +G SIP LC  + LE +G CR+C VE+E +RG+P 
Sbjct: 25  QVSLSIDGRAISVPAGTSVMRAAAMLGTSIPKLCATDSLEAFGSCRMCMVEIEGMRGYP- 83

Query: 62  LVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYG 112
             A C  PV +G+VVRT   ++  +R+ ++E  ++  P          + EL+ +A + G
Sbjct: 84  --ASCTTPVSEGMVVRTETPRLAGLRRNVMELYISDHPLDCLTCSANGNCELQTVAGQVG 141

Query: 113 ADRDR-------------------FEKHPSFCIHCGLCVRYCAEIKKKNAVGFVDRGSNR 153
               R                   F+  PS CI C  CVR C +I+   A+    RG   
Sbjct: 142 LREVRYGYDGANHLDEKKDVSNPYFDYEPSKCIVCSRCVRACEDIQGTFALTITGRGFES 201

Query: 154 EISFI--PEIAAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEA---HSGGCGCSCS 208
            ++        A EC  C  C   CPT+ L    ++    +  PE +       CG  CS
Sbjct: 202 RVAAAGGENFLASECVSCGACVQTCPTATLTEKSLVQ---LGQPERSVITTCAYCGVGCS 258


Lambda     K      H
   0.320    0.137    0.432 

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: 476
Number of extensions: 21
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 218
Length of database: 960
Length adjustment: 33
Effective length of query: 185
Effective length of database: 927
Effective search space:   171495
Effective search space used:   171495
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: 51 (24.3 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