GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Thiothrix lacustris DSM 21227

Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_084260334.1 Q394_RS0103655 carbohydrate ABC transporter permease

Query= TCDB::O30493
         (276 letters)



>NCBI__GCF_000621325.1:WP_084260334.1
          Length = 281

 Score =  358 bits (918), Expect = e-104
 Identities = 173/260 (66%), Positives = 214/260 (82%)

Query: 17  LAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINERSNYFSYAWNSV 76
           LAWAI  +IFFP+ +M +T+FKTE+ A A P  ++FTPT EN+  + ERS YF YAWNSV
Sbjct: 22  LAWAITFIIFFPLLFMFVTAFKTELQAIAVPSVWVFTPTWENFALVQERSGYFDYAWNSV 81

Query: 77  LISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVLMPIYLLAKSFGL 136
           + S  +T L LLI+VPAAYSMAF  TKRTK  L+WMLSTKM+P VG L+PIY+L ++FGL
Sbjct: 82  ITSVGSTILGLLIAVPAAYSMAFSPTKRTKDILMWMLSTKMMPAVGALLPIYVLCQTFGL 141

Query: 137 LDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIAKGG 196
           LD  I+LIII+T++NLPI+VWM+Y+ FKDIP +ILEAAR+DGA+L +E   VLLP+A GG
Sbjct: 142 LDNVISLIIIFTMMNLPIMVWMLYSNFKDIPIEILEAARMDGASLSEEFRHVLLPLAMGG 201

Query: 197 LASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAKLSAVSTLACAPIL 256
           +AST LL L+L WNEAFW LNLT++NA  L +L+ASYSSPEGLFWAKLSAVS LA API+
Sbjct: 202 MASTGLLCLVLSWNEAFWVLNLTAANAGTLASLVASYSSPEGLFWAKLSAVSVLAIAPIV 261

Query: 257 IFGWISQKQLVRGLSFGAVK 276
           +FGW SQKQLV+GL+FGAVK
Sbjct: 262 VFGWFSQKQLVQGLTFGAVK 281


Lambda     K      H
   0.327    0.137    0.426 

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: 386
Number of extensions: 13
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: 276
Length of database: 281
Length adjustment: 25
Effective length of query: 251
Effective length of database: 256
Effective search space:    64256
Effective search space used:    64256
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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