GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Shewanella sp. ANA-3

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 7026006 Shewana3_3154 putative sulfate transporter YchM (RefSeq)

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__ANA3:7026006
          Length = 590

 Score =  625 bits (1611), Expect = 0.0
 Identities = 320/567 (56%), Positives = 424/567 (74%), Gaps = 14/567 (2%)

Query: 6   SSHVMPFR---ALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGL 62
           S+H+   R   AL +AC K+KY+  RF +DL+AG+TVGIIAIPLAMALAI SGVAPQYGL
Sbjct: 8   SAHLFSLRIAHALSEACVKDKYSVKRFGQDLLAGLTVGIIAIPLAMALAIASGVAPQYGL 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 GL + H+PE Y  K+ AL  ALP+++
Sbjct: 128 RLGRLILYIPESVTLGFTAGIGVVIATLQLKDFFGLHIEHMPEQYFSKIMALGQALPSLH 187

Query: 183 VGDAAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLA 242
           +    +   TL  ++ WP+L + +P HLPA+  G  +  ++N +G  + TIG++FHY L+
Sbjct: 188 LPSLLVAAATLATMLLWPKLKLPVPAHLPAIALGSILALVLNAMGADIETIGTRFHYQLS 247

Query: 243 DGSQGNGIPQLLPQLVLPW---DLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVV 299
           DGS G GIP +LP    PW         F     + + LLPAAF++AMLGAIESLLCAVV
Sbjct: 248 DGSVGTGIPAVLPHFEWPWLQTGANGQTFEFNLATFQALLPAAFAIAMLGAIESLLCAVV 307

Query: 300 LDGMTGTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSIL 359
           LDGMTG +H ANSEL+GQG+GNII PFFGGI ATAAIARSAANV+AGA SPI+++IH+I+
Sbjct: 308 LDGMTGKRHSANSELLGQGIGNIITPFFGGIPATAAIARSAANVKAGAQSPIASMIHAIV 367

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

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

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

Query: 532 RTMARAGIQPIPGRLAFFPNRRAAMAD 558
           RT+ARA +QPI G L F+P  R A+A+
Sbjct: 548 RTLARAKVQPIEGVLKFYPTLREALAE 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: 826
Number of extensions: 32
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: 559
Length of database: 590
Length adjustment: 36
Effective length of query: 523
Effective length of database: 554
Effective search space:   289742
Effective search space used:   289742
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