GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized)
to candidate 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_25890
         (276 letters)



>FitnessBrowser__Dino:3609759
          Length = 275

 Score =  159 bits (401), Expect = 8e-44
 Identities = 91/279 (32%), Positives = 153/279 (54%), Gaps = 7/279 (2%)

Query: 1   MTLQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL 60
           MT +Q ++  S +   L  A   ++  PI W+ L +FK+ +D +    +  FTPTLEN+ 
Sbjct: 1   MTGKQRKQFWSAVHAVLIIAAMFVMLVPILWIFLAAFKSHVDVYQL--KLFFTPTLENFG 58

Query: 61  HVNE---RSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKM 117
            V +   R G   F  NS V++     + + IA  AAYS + +        L+ +L+T+ 
Sbjct: 59  TVFDDPYRLGEKLF--NSTVVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQF 116

Query: 118 LPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLD 177
           LP V +++P +++ +  GLLDTR+ LI++   I +P  +WMI  +   IP D  EAA +D
Sbjct: 117 LPAVVIILPFFIMFRDIGLLDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVD 176

Query: 178 GATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPE 237
           G++  Q +  ++LP+A  GL ++ +   I+ WNE  ++L LT+  A  L   +A +   E
Sbjct: 177 GSSRLQVIWNIVLPMAAPGLLTSGIFCFIIAWNEFLFALILTNKDAVTLPIGLALFKGEE 236

Query: 238 GLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276
           G  W  LSA   +  AP+ +   + +K  V+G++ GAV+
Sbjct: 237 GDLWNLLSAAGIIIMAPMFVLALMIRKYFVQGMTMGAVR 275


Lambda     K      H
   0.327    0.138    0.431 

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: 258
Number of extensions: 12
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: 276
Length of database: 275
Length adjustment: 25
Effective length of query: 251
Effective length of database: 250
Effective search space:    62750
Effective search space used:    62750
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 (21.8 bits)
S2: 47 (22.7 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