GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS08675 CA265_RS08675
           glucose/galactose MFS transporter
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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