GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Shewanella sp. ANA-3

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__ANA3:7024902
          Length = 320

 Score =  105 bits (261), Expect = 2e-27
 Identities = 105/356 (29%), Positives = 161/356 (45%), Gaps = 78/356 (21%)

Query: 33  LVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVG 92
           LV    F  F +G ++      TNL+  N+F++I ALGM LVI++G IDLSVG+++A  G
Sbjct: 21  LVGTFQFDGFASGRVV------TNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74

Query: 93  AIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLF 152
            + ++L  ++  +P LA ++ L +G + GA  G  I  +++  FIVTLAGM + RGL   
Sbjct: 75  VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT- 133

Query: 153 VLGGKNIG---PFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVVN 209
            L  ++I    PF      +S   LP  G ++  +   ++  V+I V + Y         
Sbjct: 134 TLSEESIAIDHPFYDAVAEMSIA-LPGNGALDLSSLIFILFFVIIAVVMHY--------- 183

Query: 210 VKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTI 269
            + G +V   G                G Q S                 L      +TTI
Sbjct: 184 TRFGTNVYAIG----------------GNQHSA---------------ELMGISIAKTTI 212

Query: 270 GRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFEL 329
              +YA+  +     L+GI     +F TF   G   G  G+                 EL
Sbjct: 213 S--IYAI--SSFLATLAGI---VFTFYTF--SGYALGAIGV-----------------EL 246

Query: 330 DVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVG-LGIDFQQMVKGLVL 384
           D IAA  IGG   +GG G + G V+G  +MGV+   ++  G L   + ++V GL+L
Sbjct: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302



 Score = 25.8 bits (55), Expect = 0.002
 Identities = 47/222 (21%), Positives = 90/222 (40%), Gaps = 37/222 (16%)

Query: 28  GMLIALVAIMVFFQFYTGGILFRPVNLT----NLILQNSFIVIMALGMLLVIVAGHIDLS 83
           G +I +  +  F     G  L R +  T    ++ + + F   +A   + +   G +DLS
Sbjct: 107 GTIIHVYKLQPFIVTLAGMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLS 166

Query: 84  VGSIVAFVGAIAAILT-VQWGMNPFLAALICLVIGGIIGAAQ-------GYWIAYHRIPS 135
               + F   IA ++   ++G N +        IGG   +A+          I+ + I S
Sbjct: 167 SLIFILFFVIIAVVMHYTRFGTNVY-------AIGGNQHSAELMGISIAKTTISIYAISS 219

Query: 136 FIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPD--IGGIEGLNTTSMILTVL 193
           F+ TLAG++     T +   G  +G    +   I+   +    + G  G    +++  +L
Sbjct: 220 FLATLAGIV----FTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVIL 275

Query: 194 ITVALFYL-------AWRRRVVNVKHGIDVEPFGFFIVQNLL 228
           + V   Y+       +W  ++V     I +  F F ++Q LL
Sbjct: 276 MGVIQTYITFDGSLSSWWTKIV-----IGLLLFFFILLQKLL 312


Lambda     K      H
   0.329    0.145    0.422 

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: 437
Number of extensions: 26
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 398
Length of database: 320
Length adjustment: 29
Effective length of query: 369
Effective length of database: 291
Effective search space:   107379
Effective search space used:   107379
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: 49 (23.5 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