GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Marinobacter adhaerens HP15

Align ABC transporter for L-Histidine, permease component (characterized)
to candidate GFF3964 HP15_3904 binding-protein-dependent transport systems inner membrane component

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



>FitnessBrowser__Marino:GFF3964
          Length = 221

 Score = 83.2 bits (204), Expect = 5e-21
 Identities = 57/165 (34%), Positives = 92/165 (55%), Gaps = 18/165 (10%)

Query: 89  WDKLMQTLALMLVATLISVLIGIPLGILSARSNRLR--------SVLMPLLDIMQTMPSF 140
           WD    TL ++ ++ L SVLIG+P+G+L     + +        +VL  ++++++++P  
Sbjct: 18  WD----TLVMVGMSLLFSVLIGLPIGVLLFLFGKRQLLEQPVAYAVLSFVVNVLRSVPFI 73

Query: 141 VYLIPVL----MLFG--LGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGAN 194
           + LI ++    ML G  LG   AI   V   AP   RL +  +R+VD  ++EA  A GA+
Sbjct: 74  ILLIVMIPFTVMLIGTSLGVAGAIPPLVAGGAPFFARLVETSLREVDRGIIEATQAMGAS 133

Query: 195 RWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGE 239
             Q +FG  LP ALP I+AGI  T +  +S   ++ +IG  GLG+
Sbjct: 134 VKQIIFGALLPEALPGIIAGITVTAITLVSYAAMSGVIGGGGLGD 178


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: 180
Number of extensions: 11
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: 283
Length of database: 221
Length adjustment: 24
Effective length of query: 259
Effective length of database: 197
Effective search space:    51023
Effective search space used:    51023
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: 46 (22.3 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