GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Halococcus hamelinensis 100A6

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate WP_007695788.1 C447_RS16060 sugar ABC transporter permease

Query= reanno::WCS417:GFF4323
         (302 letters)



>NCBI__GCF_000336675.1:WP_007695788.1
          Length = 324

 Score =  150 bits (378), Expect = 5e-41
 Identities = 94/267 (35%), Positives = 145/267 (54%), Gaps = 6/267 (2%)

Query: 32  VLVGF--YGYILWTFVLSFTNSTFLPTYKWAGL--AQYARLFDNDRWWVASKNLAVFGGM 87
           V++GF  YG I W  ++S T+ T   +  +  L    Y +   +     AS+N  V   +
Sbjct: 51  VIMGFFVYGGIGWNLLVSLTDYTGFGSADYGDLDFEMYVQALSSPDVIAASRNTFVLLVV 110

Query: 88  FIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGLDKLLR 147
           F  + LV+G+ LAI LD++IR +  I+TIYL PMALS +VT   W W+ N   G+  ++ 
Sbjct: 111 FTAVCLVLGLALAIVLDRQIRFKEQIQTIYLLPMALSFVVTAQFWLWMYNYNSGVINIIL 170

Query: 148 DWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQIDGASM 207
           D    G R+ ++ DP  V+  ++ A +WQ SG+ M ++L+GL+ + Q    AA  DGAS 
Sbjct: 171 DAVGIG-RIQFIGDPRFVLGAVIFALIWQFSGYTMIVYLSGLQSIPQDQFEAAATDGAST 229

Query: 208 PRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAG-GPGYSSDLPAMFMYSFTFS 266
            +IYW V++P L+    SA ++L   A+K+F  + +M     P   SD+ A  M    F 
Sbjct: 230 VKIYWRVIIPQLKSASVSAAVVLMIFALKAFTFLYSMFGTYRPPNGSDILATLMVRQAFK 289

Query: 267 RGQMGMGSASAILMLGAILAIIVPYLY 293
             +    +A A L+L   L +I PYLY
Sbjct: 290 FQEWSYAAAVATLLLLMALVVIGPYLY 316


Lambda     K      H
   0.330    0.141    0.455 

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: 282
Number of extensions: 19
Number of successful extensions: 3
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: 302
Length of database: 324
Length adjustment: 27
Effective length of query: 275
Effective length of database: 297
Effective search space:    81675
Effective search space used:    81675
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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