GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Sphingomonas koreensis DSMZ 15582

Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate Ga0059261_3091 Ga0059261_3091 Sugar (and other) transporter

Query= TCDB::M1Q159
         (468 letters)



>FitnessBrowser__Korea:Ga0059261_3091
          Length = 430

 Score =  216 bits (550), Expect = 1e-60
 Identities = 145/434 (33%), Positives = 221/434 (50%), Gaps = 32/434 (7%)

Query: 15  KVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74
           K I   SAG ++EWYD+Y + A     A  F+  G     ++     FAVGFL+RP G  
Sbjct: 15  KSILGGSAGNLVEWYDWYAYAAFTLYFAPHFFPKGDQTTQLLNTAAVFAVGFLMRPIGGW 74

Query: 75  VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134
           + G   D  GRK    +++++M + + LI + P  + +GA A  +L+  R++QGL++GG+
Sbjct: 75  LMGVYADKYGRKAGLTLSVSLMCAGSLLIAVTPGYETIGALAPALLVFARLMQGLSIGGE 134

Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPF 194
           YG +AT+++E A + +RGF++S+   T   G LI+LGV+LI + S+ EA    WGWR+PF
Sbjct: 135 YGASATYLSEMAGRKRRGFFSSFQYVTLISGQLIALGVLLILQASMSEAALESWGWRIPF 194

Query: 195 MASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMG 254
                L ++  W+RR L E+  F+  K  +      L     +P     V+    G T+ 
Sbjct: 195 FIGGALAVIVFWLRRGLSETQSFENAK-AEGRKTGALALLREHPGEFLLVMALTAGGTLA 253

Query: 255 QGVVWYTGQFYAL-FYLQK-IFNTPLID---SNLIVGAALLLSMPFFVFFGSLSDRIGRK 309
                    FYA   YLQK + NT   D   ++ I  AAL + M      G+LSDRIGRK
Sbjct: 254 ---------FYAYSIYLQKFLVNTSGFDRETASEINAAALFVFMCIQPLAGALSDRIGRK 304

Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVY 369
            +M+   +L VL  YPI+  +   +         +A  G   ++LG LV      VT   
Sbjct: 305 PLMIGFGVLGVLCTYPIFTALEQVSSA-------WAAFG---LMLGALVI-----VTGYT 349

Query: 370 GPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIA 429
              A    ELFP  IR   ++LPY + N +FGG    + L      G +    W+   + 
Sbjct: 350 SINAVVKAELFPAHIRTLGVALPYALANAIFGGTAEYVAL-WFKDQGMERGFYWYVTGMI 408

Query: 430 GICLVVGFLLIKET 443
           GI L+V +L +++T
Sbjct: 409 GISLIV-YLRMRDT 421


Lambda     K      H
   0.328    0.144    0.450 

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: 565
Number of extensions: 22
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: 468
Length of database: 430
Length adjustment: 33
Effective length of query: 435
Effective length of database: 397
Effective search space:   172695
Effective search space used:   172695
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 (21.7 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