GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC26dg in Pseudomonas putida KT2440

Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate PP_4112 PP_4112 Sulphate transporter

Query= TCDB::Q1J2S8
         (499 letters)



>FitnessBrowser__Putida:PP_4112
          Length = 486

 Score =  373 bits (957), Expect = e-108
 Identities = 204/473 (43%), Positives = 298/473 (63%), Gaps = 9/473 (1%)

Query: 19  ANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAAT 78
           A  R D+LAG+  + AL+PE IAF+++A ++P +GLY +FII  +TA  GGRPGMIS A 
Sbjct: 10  ARLRADLLAGLTTSFALVPECIAFALVAHLNPLMGLYGAFIICTLTALFGGRPGMISGAA 69

Query: 79  GAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAIL 138
           G+MA+++  LV  HG+QYL A  +L GV+ ++FG  +L + ++ VP  VM+GFVN LAI+
Sbjct: 70  GSMAVVIVALVVQHGVQYLLATVLLGGVVMILFGLLRLGKLVRLVPYPVMLGFVNGLAIV 129

Query: 139 IFMAQLPQFV-GANWQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAV 190
           I MAQL  F  G +W        M  +VA  +A++Y+LP + +A+P ALVAI+ + +V  
Sbjct: 130 IAMAQLEHFKDGEHWLSGTPLYLMIGLVALTMAVVYVLPKLTRAVPPALVAILGVGLVVY 189

Query: 191 VTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLID 250
           V G   +T+GDM  +   LP    P VP   ETL II P A+ +++VGLLE+LLT  L D
Sbjct: 190 VLGLPTRTLGDMAHIAGGLPGLALPDVPWNLETLKIIAPYAVLMAMVGLLETLLTLNLTD 249

Query: 251 ERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLM 310
           E T++    + E    G AN+V+G  GGM GCAMIGQ++IN++S GRGRLS  VAG  ++
Sbjct: 250 EITESRGFPDRECVALGAANMVSGLCGGMGGCAMIGQTVINLSSNGRGRLSGVVAGVMIL 309

Query: 311 VLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTH 370
           + +L L PL+ +IP+AALV VM VVA  TF W SLR L   P  + + ++A   VTV T 
Sbjct: 310 LFVLFLSPLIERIPLAALVGVMFVVAQQTFAWASLRVLHKVPVNDVLAIVAVTVVTVLT- 368

Query: 371 DLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFT 430
           DL++ VL G++++AL FA + ++       ++ +G + Y++ G LFF ST  FL+QFD  
Sbjct: 369 DLAMAVLFGIIIAALNFAWQHARELYADTHEDAEGGKCYQLHGTLFFASTTSFLNQFDTA 428

Query: 431 HPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVER 483
               +V +D     F D SAV AL  +  ++ + G  + +  L+     L++R
Sbjct: 429 GDPAQVTLDCQHLSFVDYSAVAALKTLRERYAKAGKHLRVVHLSERCKKLLKR 481


Lambda     K      H
   0.328    0.140    0.407 

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: 490
Number of extensions: 19
Number of successful extensions: 3
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: 499
Length of database: 486
Length adjustment: 34
Effective length of query: 465
Effective length of database: 452
Effective search space:   210180
Effective search space used:   210180
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 (21.7 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