GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tnaB in Shewanella loihica PV-4

Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 5210760 Shew_3188 aromatic amino acid permease (RefSeq)

Query= SwissProt::Q02DS7
         (417 letters)



>FitnessBrowser__PV4:5210760
          Length = 395

 Score =  203 bits (517), Expect = 6e-57
 Identities = 129/405 (31%), Positives = 210/405 (51%), Gaps = 19/405 (4%)

Query: 15  LLGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMILEANLNYPVG 74
           +LG   I+AGTA+G GM +LP+A + +    ++ + +  W   + + +++LE NL   VG
Sbjct: 1   MLGSIAIVAGTAIGGGMLALPLATASLGTIPALLLLVAIWGVSIYTSLLMLEINLRAGVG 60

Query: 75  SSFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGLGVTLPEKLAG 134
            +   IT   LG+   ++ G S   +L+ LT  Y+ GG S++       LG+ +  + A 
Sbjct: 61  LNVHAITGKTLGKVGQLIQGGSFLSLLFALTMVYLMGGSSLLESRFEP-LGIKVNHEAAV 119

Query: 135 LLFALA----VALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILFNSGEPD 190
           L+F L     +A+ V W    +D+++ ++   M+  F + +  LL  + P+ +      +
Sbjct: 120 LIFTLVFGGFIAIGVSW----IDKVSRVLFSAMVALFVIVVLFLLPEVSPSYILRESATE 175

Query: 191 AVYWPYL----LATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYLLW 246
            V    L    LA +P   TSFG+H  + ++++Y   D   + + L IG+ I L  Y+LW
Sbjct: 176 LVSKGELGNLWLAAIPVVFTSFGFHVCIATIVRYLDGDAMSLRKVLMIGSTIPLVCYILW 235

Query: 247 QASTLGTIPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGVTL 306
              TLGT+      G      ++  LV  L  I  SD L   +  F+NLA+ +SFLGVT+
Sbjct: 236 LMVTLGTVGGATVYGF---EGSLPKLVSALQGIAHSDILRQCIDLFANLALITSFLGVTM 292

Query: 307 GLFDYLADLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVIVP 366
            LFDY+A+L R  D+  GR +T L+TFVPP +  L +P+GFI  +GFA L      + +P
Sbjct: 293 SLFDYIAELTRARDNLLGRLQTWLITFVPPLLCALYYPDGFIKVLGFAALPLVVMIIFLP 352

Query: 367 ALMARASRKR-FGSPLFRAWGGTPAIVLVLLFGVANAVAHILASL 410
             MA   RK+  G   ++  GG  A+    L G+    A +  +L
Sbjct: 353 IAMALGQRKQNLGG--YQVSGGQFALAASALVGLVIIAAQLWVAL 395


Lambda     K      H
   0.326    0.141    0.445 

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: 503
Number of extensions: 24
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: 417
Length of database: 395
Length adjustment: 31
Effective length of query: 386
Effective length of database: 364
Effective search space:   140504
Effective search space used:   140504
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