GapMind for catabolism of small carbon sources

 

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

Align gluconate:H+ symporter (gntT) (characterized)
to candidate 7025533 Shewana3_2684 gluconate transporter (RefSeq)

Query= reanno::Cup4G11:RR42_RS28835
         (453 letters)



>FitnessBrowser__ANA3:7025533
          Length = 452

 Score =  203 bits (516), Expect = 1e-56
 Identities = 144/456 (31%), Positives = 237/456 (51%), Gaps = 19/456 (4%)

Query: 10  LLYALIAVIALVVLI-AKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTLGHI 68
           L+  LI VIA +V+  +KFKL+PF+TL++ + +  FA G+P GDI K+   G G  LG+I
Sbjct: 3   LVLILIGVIAFIVIATSKFKLHPFLTLILAAFIAAFAYGLPSGDIAKTITTGFGNILGYI 62

Query: 69  ALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGFVLL 128
            LV+ LGT++G ++ +SG A  +A  +I   G++     M  I ++V +PVF + GFV+L
Sbjct: 63  GLVIVLGTIIGIILEKSGAAITMADVVIKVLGKRFPTLTMSIIGYLVSIPVFCDSGFVIL 122

Query: 129 VPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAV--TAYKADIGKTILYAL 186
             +  ++A R   S V + + +  GL   H  +PP P  + A      ++++G  I   L
Sbjct: 123 NSLKQSMANRMKVSSVSMSVALATGLYATHTFVPPTPGPIAAAGNLGLESNLGLVIGVGL 182

Query: 187 IVGIPTAAIAGPLFAKLMTRYVTL-PD---VNPLAAQFTEEDEGVKASHELPGFGITLFT 242
           +V    AA+AG  +A    R+ ++ PD      L AQ  + +   ++   LP        
Sbjct: 183 LVA-AVAALAGMFWA---NRFASVEPDGEGAEELKAQAADFEALKQSYGTLPSPLKAFAP 238

Query: 243 ILLPVILMLIGSWADLITTP--KTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRE 300
           I +P++L+ +GS A+  + P  K      L  +G  V ALLI   +S     K      E
Sbjct: 239 IFVPILLICLGSIANFPSAPLGKEGLFSLLVFLGQPVNALLIGLFLSLLLL-KSDNKIAE 297

Query: 301 NILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVL 360
              R +   VA   II L+ GAGG FG VL+ + I + +    +   V +  + ++VA  
Sbjct: 298 FSERISQGLVAAAPII-LITGAGGAFGAVLKATPIGDFLGSSLSALGVGI-FMPFIVAAA 355

Query: 361 IRIATGSATVAMTTAAGIVAPIAASV---PGTRPELLVLTTGAGSLILSHVNDGGFWLVK 417
           ++ A GS+TVA+   + +VAP+   +         L V+  GAG++ +SH ND  FW+V 
Sbjct: 356 LKSAQGSSTVALVATSALVAPMLGDIGLGSDMGRVLTVMAIGAGAMTVSHANDSFFWVVT 415

Query: 418 EYFNMTVAQTFKTWSVCETLISVIALLLTLALATVV 453
           ++  M+V Q +K  ++   +  V A+L    L+ V+
Sbjct: 416 QFSRMSVKQAYKAQTMATLIQGVTAMLTVYVLSLVL 451


Lambda     K      H
   0.326    0.141    0.410 

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: 592
Number of extensions: 34
Number of successful extensions: 6
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: 453
Length of database: 452
Length adjustment: 33
Effective length of query: 420
Effective length of database: 419
Effective search space:   175980
Effective search space used:   175980
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 (21.6 bits)
S2: 51 (24.3 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