GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatP in Shewanella sp. ANA-3

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= TCDB::B8H230
         (332 letters)



>lcl|FitnessBrowser__ANA3:7024902 Shewana3_2076 inner membrane ABC
           transporter permease protein YjfF (RefSeq)
          Length = 320

 Score =  147 bits (370), Expect = 5e-40
 Identities = 105/300 (35%), Positives = 164/300 (54%), Gaps = 21/300 (7%)

Query: 28  TILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLA 87
           ++L  + LV  F    + F + R   N+L + +   I A+GMT VI+ GGID++VG+++A
Sbjct: 14  SLLLTMFLVGTFQF--DGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIA 71

Query: 88  FASIAAAYVVTAVVGDGPATW--LIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGM 145
            + +  + ++T         W  L+A +V   +G   G + G  +    +  FIVTL GM
Sbjct: 72  LSGVVTSLLITEY------QWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGM 125

Query: 146 TVWRG-ATLLLNDGGPISG-FNDAYRWW-----GSGEILFLPVPVVIFALVAAAGHVALR 198
            + RG AT L  +   I   F DA         G+G +    +  ++F ++ A   V + 
Sbjct: 126 FLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIA---VVMH 182

Query: 199 YTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGT 258
           YTR+G  VYA+GGN  +A L G+++   T S+YAI   LA L+G + +    S  A+   
Sbjct: 183 YTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAI 242

Query: 259 GYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVM-LHVTSYVQQVVIGLII 317
           G EL  IA+VVIGG  LTGGSG V GTVLG +L+GV+   +     ++S+  ++VIGL++
Sbjct: 243 GVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302


Lambda     K      H
   0.325    0.140    0.413 

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: 284
Number of extensions: 23
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 332
Length of database: 320
Length adjustment: 28
Effective length of query: 304
Effective length of database: 292
Effective search space:    88768
Effective search space used:    88768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 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