GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pedobacter sp. GW460-11-11-14-LB5

Align Glucose/galactose porter (characterized)
to candidate CA265_RS08675 CA265_RS08675 glucose/galactose MFS transporter

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__Pedo557:CA265_RS08675
          Length = 428

 Score =  229 bits (585), Expect = 9e-65
 Identities = 139/423 (32%), Positives = 227/423 (53%), Gaps = 26/423 (6%)

Query: 13  TETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYF 72
           T  S Q      L  +  LFF++GF+T  N  LIP  K  F L+  Q+  + F  + AYF
Sbjct: 4   TTKSGQTQGPKPLIIICALFFIFGFVTWANGTLIPFFKLSFGLSNLQAFFVTFASYMAYF 63

Query: 73  IVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQ 132
            ++LP+  ++K++ +K GIV+GL++  +G  +FIPAA  R + LFL  +FV  + + +LQ
Sbjct: 64  FLALPSSWILKKVGFKNGIVLGLVILGLGSLIFIPAAQTRTFGLFLTGIFVQGAALALLQ 123

Query: 133 VAANPYVTILGKPETAASRLTLTQAFNSLGTTVAP-VFGAVLI---------LSAATDAT 182
            A+NPY+TI+G  E+AA R+++    N     + P + G++ +         + AAT A 
Sbjct: 124 TASNPYLTIIGPIESAAKRISIAGICNKFAGMIVPLIMGSLFLKNASEVEKQIKAATGAV 183

Query: 183 ----VNAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDK-----KEGSAWQ 233
               +N     V  PY++LA+ F + AI       P+V+ +E  + +      K  S +Q
Sbjct: 184 HEQLLNDVLGRVNMPYIVLAIVFCLFAIFIKFTNLPEVEVEEDVIDESKGEVVKHKSIFQ 243

Query: 234 YRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIG 293
           + HL LGA+ IFVYVGAEV  G  +  +  +    G+S   +    +      ++G  IG
Sbjct: 244 FPHLFLGALCIFVYVGAEVMAGDIIGIYGRE---LGISPEISGKLTSITLFSMLIGYIIG 300

Query: 294 SAAM-RYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALH 352
              + +YI   KAL   A + II   ++   +   A+  V  +GL NS+M+P IF L + 
Sbjct: 301 IVTIPKYISQQKALRICAILGIIFTILSFVISSWFAVIFVALLGLANSLMWPAIFPLGIS 360

Query: 353 GLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIH--LAFLMPII-CYAYIAFYGLIG 409
            LG  T  GS I+ + I GGA++PL+   L + + ++  LA+L+ ++ CY YI ++ + G
Sbjct: 361 HLGKFTKIGSAIMIMGIAGGALMPLLYAFLNEKLHVNFQLAYLLTVLPCYLYILYFAIKG 420

Query: 410 SKS 412
            K+
Sbjct: 421 HKA 423


Lambda     K      H
   0.328    0.141    0.420 

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: 573
Number of extensions: 40
Number of successful extensions: 4
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: 412
Length of database: 428
Length adjustment: 32
Effective length of query: 380
Effective length of database: 396
Effective search space:   150480
Effective search space used:   150480
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: 50 (23.9 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