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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__MR1:202654 SO3553 sulfate permease family
           protein (NCBI ptt file)
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources