GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlA in Pontimonas salivibrio CL-TW6

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_104914290.1 C3B54_RS05650 PTS mannitol transporter subunit IICB

Query= BRENDA::P00550
         (637 letters)



>NCBI__GCF_002950575.1:WP_104914290.1
          Length = 371

 Score =  409 bits (1051), Expect = e-118
 Identities = 204/352 (57%), Positives = 260/352 (73%), Gaps = 1/352 (0%)

Query: 6   KIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIG 65
           +  +Q  G  L+ MV+PNIGAFIAWG++TALFIPTGWLPNE+ A +VGPMI  LLP+LIG
Sbjct: 16  RASLQKLGGNLAGMVIPNIGAFIAWGLLTALFIPTGWLPNESFASMVGPMILNLLPILIG 75

Query: 66  YTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSG 125
           YTGG++V G+RG V+G+I T+GVIVG D+PMFLG+MI GPL  W +K  D+ +D     G
Sbjct: 76  YTGGRIVHGQRGAVIGSIATVGVIVGTDIPMFLGAMIIGPLLAWILKQIDKVLDPITPPG 135

Query: 126 FEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAK 185
           FEML+ NFS GI GM+ A+L +L IGP V A+S +L  GV +MV + +LP+AS+ VEPAK
Sbjct: 136 FEMLIGNFSLGISGMLGAMLGYLAIGPTVSAISTVLGNGVQWMVDNSLLPIASLIVEPAK 195

Query: 186 ILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGG 245
           ILFLNNAINHG+ +PLG+ ++ E GKSI F++E NPGPG+G+L+A+   G    + SA G
Sbjct: 196 ILFLNNAINHGVLAPLGVVEAEETGKSILFMLETNPGPGLGILVAFWLAGPKILRGSAPG 255

Query: 246 AAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLA 305
           A IIHFLGGIHEIYFPYVLM P++ILA ILGG TGV T  + G GLV+  SPGSI A LA
Sbjct: 256 AIIIHFLGGIHEIYFPYVLMKPQVILAAILGGATGVATFMVTGVGLVATPSPGSIFAYLA 315

Query: 306 MTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEED-DIEAATRRMQDMK 356
           +TP+G +   + G+  + AVSFVV+  LL+ SK    D D EAA  +   MK
Sbjct: 316 VTPQGDHLGVLLGIVLSAAVSFVVAWFLLRLSKSDASDADFEAAKAKSAAMK 367


Lambda     K      H
   0.321    0.138    0.397 

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: 677
Number of extensions: 27
Number of successful extensions: 1
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: 637
Length of database: 371
Length adjustment: 34
Effective length of query: 603
Effective length of database: 337
Effective search space:   203211
Effective search space used:   203211
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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