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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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