GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolT in Escherichia coli BW25113

Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)

Query= TCDB::E1WAV3
         (456 letters)



>FitnessBrowser__Keio:18059
          Length = 491

 Score =  378 bits (971), Expect = e-109
 Identities = 197/473 (41%), Positives = 299/473 (63%), Gaps = 30/473 (6%)

Query: 1   MGGILFGYDTAVISGAIGSLTSYF----HLSPAET----GWAVSCVVVGCVIGSFSAGYL 52
           +GG+LFGYDTAVISG + SL + F    +LS +      G+ V+  ++GC+IG    GY 
Sbjct: 19  LGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYC 78

Query: 53  SKRFGRKKSLMVSALLFTISAVGTS---LSYTFTH---------------FVIYRIIGGL 94
           S RFGR+ SL ++A+LF IS VG++   L +T  +               FVIYRIIGG+
Sbjct: 79  SNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIGGI 138

Query: 95  AVGLAATVSPMYMSEVSPKNMRGRALSMQQFAIVFGQILIFYVNYKIASIAADTWLIELG 154
            VGLA+ +SPMY++E++P ++RG+ +S  QFAI+FGQ+L++ VNY IA     +WL   G
Sbjct: 139 GVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDG 198

Query: 155 WRYMFAAGIIPCILFCILVFLIPESPRWMMMIGREEETLKILTKISNEEHARHLLADIKT 214
           WRYMFA+  IP +LF +L++ +PESPRW+M  G++E+   IL KI     A   + +IK 
Sbjct: 199 WRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKH 258

Query: 215 SLQNDQLNAHQKLNYRDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEA 274
           SL + +    + L +  G    ++++G M+++ QQ  G+NV++YYAP V K +  S   A
Sbjct: 259 SLDHGRKTGGRLLMFGVG----VIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIA 314

Query: 275 LFQTIWIGVIQLIGSIIGAMIMDKMGRLSLMRKGTIGSIIGLLLTSWALYSQATGYFALF 334
           L QTI +GVI L  +++  M +DK GR  L   G +G  IG+     A Y+QA G  AL 
Sbjct: 315 LLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALL 374

Query: 335 GMLFFMIFYALSWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPY 394
            MLF++  +A+SWG   WVL+SEIFPN +R + ++I+V   W+AN+ VS  FPM+++N +
Sbjct: 375 SMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSW 434

Query: 395 LLSHFHGAFPMWIFAICCIFSYFFICRYLPETKGISLEKMESVVLAKRRKKLQ 447
           L++HFH  F  WI+    + +  F+ +++PETKG +LE++E++   + +K  Q
Sbjct: 435 LVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWEPETKKTQQ 487


Lambda     K      H
   0.329    0.141    0.436 

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: 703
Number of extensions: 26
Number of successful extensions: 5
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: 456
Length of database: 491
Length adjustment: 33
Effective length of query: 423
Effective length of database: 458
Effective search space:   193734
Effective search space used:   193734
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: 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