GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araUsh in Escherichia coli BW25113

Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate 17811 b3751 D-ribose transporter subunit (NCBI)

Query= uniprot:A0KWY4
         (313 letters)



>FitnessBrowser__Keio:17811
          Length = 296

 Score =  129 bits (325), Expect = 7e-35
 Identities = 90/286 (31%), Positives = 143/286 (50%), Gaps = 11/286 (3%)

Query: 6   IITALGLWA-VSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQ 64
           +++A+ L A VSA      T+        + +  S  +  + EA + G +L   D+Q   
Sbjct: 9   LVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNP 68

Query: 65  ENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLFLTR 124
             ++  V+    +G   ++I P         +K A +A IPV+ +DR     +    ++ 
Sbjct: 69  AKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGE---VVSH 125

Query: 125 IASDFSEEGRKIGQWLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRS 184
           IASD    G+  G ++  K      + ELQG  G +AA +R  GF Q +A +    ++ S
Sbjct: 126 IASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAH-KFNVLAS 184

Query: 185 QTGEFTRAKGKEVMEGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSV 244
           Q  +F R KG  VM+  L A     + AV++ NDEMALGA++A++ AG     D+++V  
Sbjct: 185 QPADFDRIKGLNVMQNLLTAH--PDVQAVFAQNDEMALGALRALQTAG---KSDVMVVGF 239

Query: 245 DGVPDYFKAMADGDVNATV-ELSPYLGGPAFDAIDAYLKGNKDQAK 289
           DG PD  KA+ DG + AT+ +L   +G    +  D  LKG K QAK
Sbjct: 240 DGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAK 285


Lambda     K      H
   0.316    0.131    0.376 

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: 205
Number of extensions: 12
Number of successful extensions: 5
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: 313
Length of database: 296
Length adjustment: 27
Effective length of query: 286
Effective length of database: 269
Effective search space:    76934
Effective search space used:    76934
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: 48 (23.1 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