GapMind for catabolism of small carbon sources

 

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

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 202654 SO3553 sulfate permease family protein (NCBI ptt file)

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__MR1:202654
          Length = 588

 Score =  624 bits (1608), Expect = 0.0
 Identities = 323/567 (56%), Positives = 427/567 (75%), Gaps = 14/567 (2%)

Query: 6   SSHVMPFR---ALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGL 62
           S+H+   R   AL +AC K++Y+  RF +DL+AG+TVGIIAIPLAMALAI SGV PQYGL
Sbjct: 8   SAHLFSLRIAHALNEACVKDRYSFKRFGQDLLAGLTVGIIAIPLAMALAIASGVPPQYGL 67

Query: 63  YTAAVAGIVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLA 122
           YTA V G +IA+TGGSR+SVSGPTAAFVV+LYP++QQFGLAGLL+AT++SG+ L+ M + 
Sbjct: 68  YTAIVGGFIIAMTGGSRYSVSGPTAAFVVLLYPIAQQFGLAGLLIATVMSGMMLVAMAML 127

Query: 123 RFGRLIEYIPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTIN 182
           R GRLI YIP SVTLGFT+GIG+ I T+Q+KDF GLQ+ H+PE Y  K+ AL  ALP+++
Sbjct: 128 RLGRLILYIPESVTLGFTAGIGVVIATLQLKDFFGLQIEHMPEQYFAKLMALGQALPSLH 187

Query: 183 VGDAAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLA 242
           +    I   TL  ++ WPRL I +P HLPA+  G  +  I+N +G  + TIG++FHY L 
Sbjct: 188 LPSLFIAAATLATMLLWPRLKIPVPAHLPAIALGSILALILNAMGAEIETIGTRFHYQLT 247

Query: 243 DGSQGNGIPQLLPQLVLPW--DLPNSE-FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVV 299
           DG  G+GIP +LP    PW    PN + F     + + LLPAAF++AMLGAIESLLCAVV
Sbjct: 248 DGGIGSGIPAVLPHFEWPWLQTGPNGQAFEFNLAAFQALLPAAFAIAMLGAIESLLCAVV 307

Query: 300 LDGMTGTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSIL 359
           LDGMTG +H ANSEL+GQG+GNIIAPFFGGI ATAAIARSAANV+AGA SPI+++IH+++
Sbjct: 308 LDGMTGKRHSANSELLGQGIGNIIAPFFGGIPATAAIARSAANVKAGAQSPIASMIHALV 367

Query: 360 VILALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTV 419
           V++ L+ LA +L++LP+SAMAALLL+VAWNMSEA K V LL+ AP  DI+V L C SLTV
Sbjct: 368 VLIGLVALAGILAYLPMSAMAALLLVVAWNMSEAPKAVHLLKTAPTSDILVFLSCFSLTV 427

Query: 420 LFDMVIAISVGIVLASLLFMRRIARMTRLAPV-----VVD--VPDDVLVLRVIGPLFFAA 472
           +FDMVIAISVGI+LA+LLFM+ IA MT+L  +      VD  +P D  VL++ GPLFFAA
Sbjct: 428 IFDMVIAISVGIILAALLFMKEIAEMTKLYDISSNKRYVDQSLPADWAVLKINGPLFFAA 487

Query: 473 AEGLFTDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLP-EGCELRVCNVEFQPL 531
           A+ +F ++ S  + K++++L  D V +LDAGGL A  + +++      +L + +++FQP+
Sbjct: 488 ADRIFAEIASLTQDKQVIVLYLDGVSILDAGGLAALSKLIEKCKLNQTKLLITDLQFQPI 547

Query: 532 RTMARAGIQPIPGRLAFFPNRRAAMAD 558
           RT+A+A IQP+ G L F+P  R A+ +
Sbjct: 548 RTLAKAKIQPVEGVLKFYPTLREALTE 574


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: 817
Number of extensions: 36
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: 588
Length adjustment: 36
Effective length of query: 523
Effective length of database: 552
Effective search space:   288696
Effective search space used:   288696
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