GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for L-Histidine, permease component (characterized)
to candidate 8500288 DvMF_1044 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_09615
         (283 letters)



>FitnessBrowser__Miya:8500288
          Length = 280

 Score =  267 bits (682), Expect = 2e-76
 Identities = 142/267 (53%), Positives = 185/267 (69%)

Query: 10  IADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRK 69
           +  W+   +D LVT+     R  S      +  LE  L   P  L++A VG +AW  TR+
Sbjct: 10  LGQWLEAAIDFLVTHLAPATRAFSAVTESGLNLLEAGLDALPPLLVIAFVGLVAWRVTRQ 69

Query: 70  VLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMP 129
           V      V  L LV  +GLW   M TLAL+LVATL++VL+GIPLGI +A S+R R+V+MP
Sbjct: 70  VALGVFAVAGLALVWNMGLWQATMSTLALVLVATLLAVLVGIPLGIAAAMSDRARAVVMP 129

Query: 130 LLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAIN 189
           +LD+MQTMP+FVYLIP +  FGLGKV A+FATVI+A PP IR T LGIRQV  E++E   
Sbjct: 130 VLDVMQTMPAFVYLIPAIPFFGLGKVAAVFATVIFAMPPAIRFTCLGIRQVPAELVECAE 189

Query: 190 AFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLN 249
           AFG  R+Q+L  ++LPLA P+++AG+NQT M+ALSMVVIA+MIGARGLG +V   IQ L 
Sbjct: 190 AFGTGRFQRLVKLELPLAAPTMLAGVNQTVMLALSMVVIAAMIGARGLGGEVWKAIQRLE 249

Query: 250 VGRGLEAGLAIVILAVVIDRITQAYGR 276
           +G G EAG+ IVI+A+ +DRI Q  G+
Sbjct: 250 MGNGFEAGIGIVIVAICLDRILQHVGK 276


Lambda     K      H
   0.328    0.142    0.429 

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: 303
Number of extensions: 10
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: 283
Length of database: 280
Length adjustment: 26
Effective length of query: 257
Effective length of database: 254
Effective search space:    65278
Effective search space used:    65278
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 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