GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Pseudomonas stutzeri RCH2

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate GFF3178 Psest_3240 Sulfate permease and related transporters (MFS superfamily)

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__psRCH2:GFF3178
          Length = 576

 Score =  506 bits (1304), Expect = e-148
 Identities = 278/548 (50%), Positives = 372/548 (67%), Gaps = 20/548 (3%)

Query: 18  ACWKEKYTAARFTR----DLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIA 73
           + W++       TR    D+ AG+TVGIIAIPLAMALAI  GVAPQ+GLYT  VA  +IA
Sbjct: 8   SAWRQALRLGYGTRALRGDISAGLTVGIIAIPLAMALAIAVGVAPQHGLYTVLVAAPLIA 67

Query: 74  LTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPV 133
           LTGGSRF+VSGPTAAFVVIL P++QQFGL GLL+ T+L+G+ LI +GL R GRLI +IP 
Sbjct: 68  LTGGSRFNVSGPTAAFVVILLPITQQFGLGGLLLCTMLAGLILITLGLLRAGRLIAFIPY 127

Query: 134 SVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTL 193
            VTLGFT+GIGI I T+QIKD  GL +   P+HY+++V  L  +LP   +GDA +  + L
Sbjct: 128 PVTLGFTAGIGIVIATLQIKDLFGLTLTEQPQHYVEQVSLLLRSLPGAQLGDAVVAAICL 187

Query: 194 GILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQL 253
            +L+ WPR   ++PGHL AL  G     ++  +G  VAT+G +F Y L DG    GIP  
Sbjct: 188 AVLIIWPRWVPKVPGHLVALTVGALAGLLLESVGLSVATLGERFSYTL-DGVTHPGIPPF 246

Query: 254 LPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKA 310
           LP    PW LP  +     L+++  R LL  AF++AMLGAIESLLCAVV DGMTG+ H+ 
Sbjct: 247 LPDFAWPWLLPGPDGQPLQLSYELFRQLLAPAFAIAMLGAIESLLCAVVADGMTGSNHEP 306

Query: 311 NSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPL 370
           N EL+GQGLGN++AP FGGITATAAIARSA NVRAGA SP++++IH+ +V++A+L LAPL
Sbjct: 307 NGELIGQGLGNLVAPLFGGITATAAIARSATNVRAGAFSPLASMIHAGVVLVAILWLAPL 366

Query: 371 LSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVG 430
            S+LP++A+AALL+MVAWNMSEA  VV +LR AP+ D++V+L C+ LTVLFDMV+A+ VG
Sbjct: 367 FSYLPMAALAALLVMVAWNMSEAPHVVHVLRIAPRSDVLVLLTCLILTVLFDMVLAVGVG 426

Query: 431 IVLASLLFMRRIARMTRLAP-------VVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESR 483
           ++LA+ LF++R++ +T           ++ D+P+ V    + GPLFF AAE     L   
Sbjct: 427 LLLAAGLFIKRMSELTDTTALSRDQRRLLQDMPEHVATYAIRGPLFFGAAEKALGALRRF 486

Query: 484 LEGKRIVILKWDAVPVLDAGGLDAFQRFV---KRLPEGCELRVCNVEFQPLRTMARAGIQ 540
               ++VI+   AVP+LD   L A +  +   +RL  G  L +     +    + RAGI 
Sbjct: 487 NPEVKVVIVDISAVPMLDMTALAALENVLVDYRRL--GVTLILSGSNARVRLKLRRAGIH 544

Query: 541 PIPGRLAF 548
            + G L +
Sbjct: 545 RLQGHLLY 552


Lambda     K      H
   0.328    0.142    0.425 

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: 782
Number of extensions: 37
Number of successful extensions: 5
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: 559
Length of database: 576
Length adjustment: 36
Effective length of query: 523
Effective length of database: 540
Effective search space:   282420
Effective search space used:   282420
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: 53 (25.0 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