GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Desulfotomaculum hydrothermale Lam5

Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_008412465.1 DESHY_RS10040 carbohydrate ABC transporter permease

Query= TCDB::O30493
         (276 letters)



>NCBI__GCF_000315365.1:WP_008412465.1
          Length = 279

 Score =  192 bits (489), Expect = 5e-54
 Identities = 99/272 (36%), Positives = 155/272 (56%), Gaps = 1/272 (0%)

Query: 6   SRRLQSLLLGTLAWAIAIL-IFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINE 64
           +R+L + +L   A AIA++    PI WMVL+S KTE + F+ PP+F F PT   Y  +  
Sbjct: 8   TRKLIATVLIYTALAIAMVWALLPIIWMVLSSLKTEANMFSMPPKFTFKPTFSTYAFMFT 67

Query: 65  RSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVL 124
             N+ S+  NS++ +FS+TA+ L++     Y++A    +R K    W++ST+M P    +
Sbjct: 68  EGNFGSFLKNSMIAAFSSTAIALILGTLGGYALARGNYRRGKDIAFWIISTRMTPVAAAI 127

Query: 125 MPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQE 184
           +P+Y++   F L+ T   L+  YT  NLP  +WM+ T+F ++P D+  AA +DGAT +Q 
Sbjct: 128 VPLYIIFAKFNLIGTTFGLVFAYTTFNLPFALWMMMTFFAELPPDMEHAAMVDGATKFQA 187

Query: 185 MVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAKL 244
             R+ LP    GL +T +L L+  WN+  ++   TS +   +    +   S  G+ W + 
Sbjct: 188 FYRIALPQVTPGLVATGILCLMFAWNDFAFASVFTSHSNQTIPVAASLLVSQTGIAWGQA 247

Query: 245 SAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276
            A  T+   P+LI G   +K LVRGLS GAVK
Sbjct: 248 MATGTVIITPMLIAGLAVRKYLVRGLSMGAVK 279


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: 296
Number of extensions: 2
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: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
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 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