GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC1A4 in Shewanella oneidensis MR-1

Align neutral amino acid transporter A (characterized)
to candidate 201109 SO1948 sodium:dicarboxylate symporter family protein (NCBI ptt file)

Query= CharProtDB::CH_091534
         (532 letters)



>FitnessBrowser__MR1:201109
          Length = 437

 Score =  207 bits (527), Expect = 6e-58
 Identities = 136/402 (33%), Positives = 209/402 (51%), Gaps = 44/402 (10%)

Query: 74  YLAFPGEMLLRMLRMIILPLVVCSLVSGAASL-DASCLGRLGGIAVAYFGLTTLSASALA 132
           +L   G + +  L+M+++PLV  SLV G  SL + S LGRLGG  +A++  TT+ A  LA
Sbjct: 47  FLHVIGTIFISSLKMLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTVLALVLA 106

Query: 133 VALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKETVDSFLDLARNLFPSNLVVAAFRTYA 192
           V  A I+ PG    TL +  L         V KE   SF  +  ++ P+N          
Sbjct: 107 VFAAVIVHPGDA--TLANEKLNY-------VAKE-APSFAQVIIDMMPTN---------- 146

Query: 193 TDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLVLFALVLGVALKKLGSEGEDLIRFFN 252
                               P+    EG N+L +++FA++ G A+  LG  G  + + F+
Sbjct: 147 --------------------PVQAMSEG-NMLQIIIFAVIFGFAIAHLGERGNRIAQLFD 185

Query: 253 SLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMKDIIVLVTSLGKYIFASILGHVIHGGIV 312
            LN   M +V+ +M   P G+  L+    + +   +    S+ KY F  +   +IH  + 
Sbjct: 186 DLNNVIMRVVTLVMQLAPYGVFALMAKLALTLG--LETFGSVVKYFFLVLTLLLIHNFVT 243

Query: 313 LPLIYFVFTRKNPFRFLLGLLAPFATAFATCSSSATLPSMMKCIEENNGVDKRISRFILP 372
             ++   F+  NP  F+  +      AF+T SS+ATLP  ++  E   GVD +I+ F LP
Sbjct: 244 YSILLKAFSGLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASFTLP 303

Query: 373 IGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQIFTILVTATASSVGAAGVPAGGVLTIA 432
           +GAT+NMDG AI Q VA VFIAQ+  +EL+      ++VTAT +S+G AGVP  G++ +A
Sbjct: 304 LGATINMDGTAIMQGVATVFIAQVFGIELSLTDYAAVIVTATLASIGTAGVPGVGLIMLA 363

Query: 433 IILEAIGLPTHDLPLILAVDWIVDRTTTVVNVEGDALGAGIL 474
           ++L  +GLP   + LI+ VD ++D   T VNV GD +   I+
Sbjct: 364 MVLNQVGLPVEGIALIIGVDRLLDMVRTAVNVTGDCVATVII 405


Lambda     K      H
   0.320    0.136    0.390 

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: 347
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 532
Length of database: 437
Length adjustment: 34
Effective length of query: 498
Effective length of database: 403
Effective search space:   200694
Effective search space used:   200694
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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