GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Sinorhizobium meliloti 1021

Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b20929 SM_b20929 sugar uptake ABC transporter permease

Query= uniprot:A0KWY7
         (320 letters)



>FitnessBrowser__Smeli:SM_b20929
          Length = 332

 Score =  158 bits (400), Expect = 2e-43
 Identities = 98/314 (31%), Positives = 174/314 (55%), Gaps = 13/314 (4%)

Query: 10  WITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAV 69
           W+  +++L    + +   D FA+ + + N+ R+  F+ I ALGMTLVII+GGIDLSVG+V
Sbjct: 27  WVLVAVILACLFL-SIATDSFATAKNLYNITRNFTFVAIIALGMTLVIITGGIDLSVGSV 85

Query: 70  IALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLAR 129
           + L  +V ++++    +   +     +    + GA  G +I      PF++TL  + +AR
Sbjct: 86  LCLCSMVLAVVM-HAGYGIEVGIAASIGTALVAGAFNGVMIAYLGFPPFVITLGMLSIAR 144

Query: 130 GLATTLSEESIAIDH-PFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAV----VMHYT 184
            LA   S  ++  +  P +D +  +     G GA  L     +L+ +++A+    V+ +T
Sbjct: 145 SLAMVASNNTVVFEFGPDHDTLLAL-----GGGAWFLGIANPVLYMIVLALLTGFVLRWT 199

Query: 185 RFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGV 244
           +FG  V+AIGGN+H+A L G+ + +  +++Y IS+  A +AGI+ T +  +       G+
Sbjct: 200 KFGRYVFAIGGNEHAATLTGVPVRRIKVAVYMISALAAGIAGIIQTGWLGAVTTNIGAGM 259

Query: 245 ELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFF 304
           EL  IAA VIGG  L GG+G   G ++G  L+ VI+  +   G ++++W    IG  +  
Sbjct: 260 ELQVIAAAVIGGANLAGGAGTASGALIGAALIEVIRNSLGLLG-INAFWQGAFIGGAIVL 318

Query: 305 FILLQKLLNGRKTQ 318
            +L  ++ N R+++
Sbjct: 319 AVLFDRIRNFRQSE 332


Lambda     K      H
   0.330    0.145    0.424 

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: 345
Number of extensions: 26
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: 320
Length of database: 332
Length adjustment: 28
Effective length of query: 292
Effective length of database: 304
Effective search space:    88768
Effective search space used:    88768
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: 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 (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