GapMind for catabolism of small carbon sources

 

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

Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate 7025533 Shewana3_2684 gluconate transporter (RefSeq)

Query= SwissProt::A0A0H2VAP9
         (445 letters)



>FitnessBrowser__ANA3:7025533
          Length = 452

 Score =  216 bits (550), Expect = 1e-60
 Identities = 150/453 (33%), Positives = 240/453 (52%), Gaps = 18/453 (3%)

Query: 7   VVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFL 66
           +V  L+  I  IV+   KFK HPFL L+LA+F      G+   D+   I +G G  LG++
Sbjct: 3   LVLILIGVIAFIVIATSKFKLHPFLTLILAAFIAAFAYGLPSGDIAKTITTGFGNILGYI 62

Query: 67  AAVIGLGTILGKMMEVSGAAERIG-LTLQRCRWLSADVIMVLVGLICGITLFVEVGVVLL 125
             VI LGTI+G ++E SGAA  +  + ++        + M ++G +  I +F + G V+L
Sbjct: 63  GLVIVLGTIIGIILEKSGAAITMADVVIKVLGKRFPTLTMSIIGYLVSIPVFCDSGFVIL 122

Query: 126 IPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLG--ADIGSVIVYGL 183
             L  S+A +   S + +++ L T L A H  VPP P  +  A  LG  +++G VI  GL
Sbjct: 123 NSLKQSMANRMKVSSVSMSVALATGLYATHTFVPPTPGPIAAAGNLGLESNLGLVIGVGL 182

Query: 184 LVGLMASLIGGPLFLKFLGQR------LPFKPVPTEFADLKVRDEKTLPSLGATLFTVLL 237
           LV  +A+L G     +F             K    +F  LK +   TLPS       + +
Sbjct: 183 LVAAVAALAGMFWANRFASVEPDGEGAEELKAQAADFEALK-QSYGTLPSPLKAFAPIFV 241

Query: 238 PIALMLVKTIAELNMA--RESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTML 295
           PI L+ + +IA    A   + GL++LL F+G P+ A  I +F++  +L ++    +    
Sbjct: 242 PILLICLGSIANFPSAPLGKEGLFSLLVFLGQPVNALLIGLFLS--LLLLKSDNKIAEFS 299

Query: 296 THTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHA 355
                G  + A I+LI GAGGAF A+LK++ + D L   LS + +  I + ++VA  L +
Sbjct: 300 ERISQGLVAAAPIILITGAGGAFGAVLKATPIGDFLGSSLSALGV-GIFMPFIVAAALKS 358

Query: 356 AVGSATVAMMGATAIVAPML---PLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYC 412
           A GS+TVA++  +A+VAPML    L  D+   +  +AIG+GA+  +   DS FW+V Q+ 
Sbjct: 359 AQGSSTVALVATSALVAPMLGDIGLGSDMGRVLTVMAIGAGAMTVSHANDSFFWVVTQFS 418

Query: 413 GATLNETFKYYTTATFIASVIALAGTFLLSFII 445
             ++ + +K  T AT I  V A+   ++LS ++
Sbjct: 419 RMSVKQAYKAQTMATLIQGVTAMLTVYVLSLVL 451


Lambda     K      H
   0.328    0.142    0.417 

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: 513
Number of extensions: 32
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: 445
Length of database: 452
Length adjustment: 33
Effective length of query: 412
Effective length of database: 419
Effective search space:   172628
Effective search space used:   172628
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: 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