GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC1A4 in Shewanella loihica PV-4

Align neutral amino acid transporter A (characterized)
to candidate 5209774 Shew_2227 sodium:dicarboxylate symporter (RefSeq)

Query= CharProtDB::CH_091534
         (532 letters)



>FitnessBrowser__PV4:5209774
          Length = 439

 Score =  219 bits (559), Expect = 1e-61
 Identities = 138/427 (32%), Positives = 222/427 (51%), Gaps = 46/427 (10%)

Query: 51  GVLAGAGLGAALRGLSLSRTQVT--YLAFPGEMLLRMLRMIILPLVVCSLVSGAASL-DA 107
           G+L G  L +   G       +T   L   G + +  L+M+++PLV  SLV G  SL D 
Sbjct: 22  GILTGLLLRSFFPGSEFIEEYITNGLLNVVGSIFISSLQMLVVPLVFISLVCGTCSLSDP 81

Query: 108 SCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKET 167
           S LGRLGG  +A++  TT  A ++A+ +A ++ PG+ +   ++    ++++         
Sbjct: 82  SSLGRLGGKTIAFYLFTTAIALSMAILVALLVHPGNASLAAENMQYSVKEA--------- 132

Query: 168 VDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLV 227
             S  D+  NL P N                              PI    EG N+L ++
Sbjct: 133 -PSLSDVLINLVPRN------------------------------PIQAMTEG-NMLQII 160

Query: 228 LFALVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMKDI 287
           +FA++ G A+  +G  G+ +   FN LNE  M +V+ IM   P GI  L+G   + +   
Sbjct: 161 IFAVIFGFAISHIGERGKRVSALFNDLNEVIMRVVTLIMQLAPYGIFALMGKLALTLG-- 218

Query: 288 IVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATCSSSA 347
           +    S+ KY    +   ++H  +  P++  +F+  +PF F+  +      AF+T SS+A
Sbjct: 219 LETFESVVKYFMVVLAVLLVHAFVSYPVLLKLFSGLSPFTFIRKMRDVQLFAFSTASSNA 278

Query: 348 TLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQIF 407
           TLP  ++  E   GVD +++ F LP+GAT+NMDG AI Q VA VFIAQ+  ++L      
Sbjct: 279 TLPVTLETSEHRLGVDNKVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYA 338

Query: 408 TILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVNVEGD 467
            ++VTAT +S+G AGVP  G++ +A++L  +GLP   + LI+ VD ++D   T VNV GD
Sbjct: 339 MVVVTATLASIGTAGVPGVGLIMLAMVLNQVGLPVEGIALIMGVDRLLDMVRTAVNVTGD 398

Query: 468 ALGAGIL 474
           ++   I+
Sbjct: 399 SVATVII 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: 322
Number of extensions: 8
Number of successful extensions: 4
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: 532
Length of database: 439
Length adjustment: 34
Effective length of query: 498
Effective length of database: 405
Effective search space:   201690
Effective search space used:   201690
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