GapMind for catabolism of small carbon sources

 

Aligments 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)



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