GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Dinoroseobacter shibae DFL-12

Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__Dino:3609043
          Length = 327

 Score =  176 bits (447), Expect = 6e-49
 Identities = 99/304 (32%), Positives = 171/304 (56%), Gaps = 4/304 (1%)

Query: 35  EYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGS 94
           E  LI   +++ A ++     F +  N+  +    S + +++   M  + +R  DLSV +
Sbjct: 10  ETLLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAA 69

Query: 95  TVAFAGVLCAMV-LNATGNTFIAIVA-AVAAGGVIGFVNGAVIAYLRINALITTLATMEI 152
            +A  G++ +MV + A G   + I+A A+  G ++G  NG ++  L+I  ++ TL TM I
Sbjct: 70  NLALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTI 129

Query: 153 VRGLGFIVSHGQAVGVS--SDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRN 210
            RG+ F++S G+ V     S  F A       G+ +  W+ +L  I+F +++ +T  GR 
Sbjct: 130 FRGIIFLISDGKWVNSHEMSPAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTTLGRA 189

Query: 211 TLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVI 270
             A GGNP A+  AGI+V +T+ + F I GA+  L G +  SR      + A GFEL+V+
Sbjct: 190 FYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVV 249

Query: 271 SACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQ 330
           +ACV+GGVS++GG  T+ G ++G L +G ++N + +++I  F+Q  + G  ++ AV L+ 
Sbjct: 250 AACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALNA 309

Query: 331 LKNR 334
             NR
Sbjct: 310 QANR 313


Lambda     K      H
   0.326    0.139    0.396 

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: 251
Number of extensions: 12
Number of successful extensions: 2
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: 338
Length of database: 327
Length adjustment: 28
Effective length of query: 310
Effective length of database: 299
Effective search space:    92690
Effective search space used:    92690
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: 49 (23.5 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