GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Klebsiella michiganensis M5al

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate BWI76_RS06705 BWI76_RS06705 binding-protein-dependent transport system inner membrane protein

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__Koxy:BWI76_RS06705
          Length = 283

 Score =  119 bits (299), Expect = 5e-32
 Identities = 72/210 (34%), Positives = 118/210 (56%), Gaps = 6/210 (2%)

Query: 63  FQNSVVLAVSATLLSALVGSLNGYVLAKWPFRG--SGLLFALILFGMFIPYQSILIPLFQ 120
           + NS+ ++    +L+ +  S   Y  +++ F+G  +GL+  L+L    IP  S LI +F 
Sbjct: 76  YWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLL--QMIPQFSALIAIFV 133

Query: 121 FMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVI 180
             + +GL  S   LVL++V   IP+ T + + Y   IP +L E+AR+DGA  F IF  +I
Sbjct: 134 LSQLLGLINSHLALVLIYVGGMIPMNTWLMKGYLDAIPKDLDESARMDGASSFRIFFEII 193

Query: 181 LPLSVPAFVVVAIWQFTQIWNEFLFAVTLTR-PESQPITVALAQLAGGE-AVKWNLPMAG 238
           +PLS P   VVA++ FT    +F+ + T+ R P+   + + L  L   +    +    AG
Sbjct: 194 MPLSKPILAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGASYTTYAAG 253

Query: 239 AILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           A+L A+P  ++Y+ L +YF+ GL +GS KG
Sbjct: 254 AVLIAVPVAILYLALQKYFVSGLTSGSTKG 283


Lambda     K      H
   0.330    0.146    0.461 

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: 175
Number of extensions: 9
Number of successful extensions: 2
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: 268
Length of database: 283
Length adjustment: 25
Effective length of query: 243
Effective length of database: 258
Effective search space:    62694
Effective search space used:    62694
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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