GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Dinoroseobacter shibae DFL-12

Align Inner-membrane translocator (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= uniprot:A0KWY7
         (320 letters)



>FitnessBrowser__Dino:3609043
          Length = 327

 Score =  139 bits (350), Expect = 9e-38
 Identities = 95/310 (30%), Positives = 156/310 (50%), Gaps = 11/310 (3%)

Query: 11  ITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVI 70
           + A++LL + L+ + +F  F +   + ++  D + L++ A+G  +VI++  IDLSV A +
Sbjct: 13  LIAAILLLLALIAS-RFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANL 71

Query: 71  ALSGVVTSLLITEYQWHPLLAFVVI-LPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLAR 129
           AL+G+V S++       P++  + I + LGTL G   G ++   ++ P +VTL  M + R
Sbjct: 72  ALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFR 131

Query: 130 GLATTLSEESIAIDH---PFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRF 186
           G+   +S+      H   P + A     +       L + S I IL  ++  +VM  T  
Sbjct: 132 GIIFLISDGKWVNSHEMSPAFKAFPRAELL-----GLPVLSWIAILAVILFTIVMTRTTL 186

Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246
           G   YA GGN H+A   GI + KT    + IS  LA L G ++       Y   A G EL
Sbjct: 187 GRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFEL 246

Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFI 306
           D +AA VIGG  + GG G V G +LG + +G+I+  +     +S +W   + G  +   +
Sbjct: 247 DVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPV-VDISPFWQLAISGGAIIIAV 305

Query: 307 LLQKLLNGRK 316
            L    N +K
Sbjct: 306 ALNAQANRKK 315


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: 340
Number of extensions: 21
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: 320
Length of database: 327
Length adjustment: 28
Effective length of query: 292
Effective length of database: 299
Effective search space:    87308
Effective search space used:    87308
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