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

GapMind for catabolism of small carbon sources

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

Align SmoE, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 3607562 Dshi_0974 extracellular solute-binding protein family 1 (RefSeq)

Query= TCDB::O30831
         (436 letters)



>FitnessBrowser__Dino:3607562
          Length = 435

 Score =  600 bits (1546), Expect = e-176
 Identities = 297/430 (69%), Positives = 338/430 (78%), Gaps = 3/430 (0%)

Query: 7   ALMGACAVAALSSAAGA-ETITVATVNNGDMIRMQGLMSEFNAQHPDITVEWVTLEENVL 65
           AL  A A+  +SS A A E + +ATVNNGDMIRMQGL  +F  +    TVEWVTLEENVL
Sbjct: 6   ALYAATALTLVSSGAMASENLVIATVNNGDMIRMQGLTQDFTDKTGH-TVEWVTLEENVL 64

Query: 66  RQKVTTDIATKGGQFDVLTIGTYEVPIWGKQGWLVSLNDLPPEYDADDILPAIRNGLTVD 125
           RQ+VTTDIA KGG FD++TIG YE PIWG  GWLV L+DL  +Y+ADDILPA+R GL+ D
Sbjct: 65  RQRVTTDIAAKGGSFDIMTIGMYETPIWGANGWLVPLDDLSADYNADDILPAMRAGLSHD 124

Query: 126 GELYAAPFYGESSMIMYRKDLMEKAGLTMPDAPTWDFVKEAAQKMTDKDAEVYGICLRGK 185
           G LYAAPFYGESSMIMYRKDLMEKAGL MPDAPTW F++EAA  MTD++ ++ GICLRGK
Sbjct: 125 GTLYAAPFYGESSMIMYRKDLMEKAGLEMPDAPTWQFIREAAAAMTDRENDINGICLRGK 184

Query: 186 AGWGENMAFLSAMANSYGARWFDENWQPQFDGEAWKATLTDYLDMMTNYGPPGASKNGFN 245
           AGWGE  AF++  ANS+GARWFDE+W  QFD   WK  L  ++ MM   GP G + NGFN
Sbjct: 185 AGWGEGGAFITVTANSFGARWFDEDWNAQFDQPEWKEALEFFVGMMNESGPNGYATNGFN 244

Query: 246 ENLALFQQGKCGMWIDATVAASFVTNPEESTVADKVGFALAPDT-GKGKRANWLGAWNLA 304
           ENL LFQQGKCGMWIDATVAASFVTNP +STVAD+VGFALAP++ G  KRANWL AW LA
Sbjct: 245 ENLNLFQQGKCGMWIDATVAASFVTNPNDSTVADQVGFALAPNSEGIEKRANWLWAWALA 304

Query: 305 IPAGSQKVDAAKQFIAWATSKDYAELVASKEGWANVPPGTRTSLYENPEYQKVPFAKMTL 364
           IPAG+QK DAAK+FI WATS DY ELVA+ EGWANVPPG RTSLYEN  Y+ +PFAKMTL
Sbjct: 305 IPAGTQKADAAKEFIEWATSTDYIELVAANEGWANVPPGARTSLYENENYKDIPFAKMTL 364

Query: 365 DSINAADPTHPAVDPVPYVGVQFVAIPEFQGIGTAVGQQFSAALAGSMSAEQALQAAQQF 424
           DSI AADPT P VDPVPYVG+QFVAIPEF GI T V Q+FSA  AG  + E+AL+ AQ  
Sbjct: 365 DSILAADPTDPTVDPVPYVGIQFVAIPEFAGIATEVSQEFSAVYAGQQTVEEALEKAQAL 424

Query: 425 TTREMTRAGY 434
           T   M  AGY
Sbjct: 425 TNDAMEAAGY 434


Lambda     K      H
   0.316    0.131    0.400 

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: 737
Number of extensions: 21
Number of successful extensions: 3
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: 436
Length of database: 435
Length adjustment: 32
Effective length of query: 404
Effective length of database: 403
Effective search space:   162812
Effective search space used:   162812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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