GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluD in Lactobacillus silagei IWT126

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate WP_054653757.1 CES79_RS00820 amino acid ABC transporter permease

Query= TCDB::P48245
         (273 letters)



>NCBI__GCF_002217945.1:WP_054653757.1
          Length = 217

 Score =  120 bits (300), Expect = 3e-32
 Identities = 66/216 (30%), Positives = 128/216 (59%), Gaps = 6/216 (2%)

Query: 16  FINSQTWTT--YILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETF 73
           F+++ +W    Y+L GLW T+  +V S+I + ++G+ LG+ R   I+++     + I+  
Sbjct: 4   FLDAYSWINIHYLLQGLWITVAVSVVSIIGSYILGSILGIIRYVNIKVVSPVIGLFIDII 63

Query: 74  RAIPVLILMIFAYQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQK 133
           R +P+L+++ F Y         PSS  A    +F +T++  ++IAEI+RSGI ++  GQ 
Sbjct: 64  RNLPLLLIIFFTYFGLPNLGFRPSSVWA---TIFAMTIFESTMIAEIVRSGIVAVDPGQM 120

Query: 134 EAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSA 193
           E A A G++  Q  + I+LPQA+  M+PAL+SQ +  +KD++L   I   +++ +     
Sbjct: 121 EGARANGLTYGQALYHIILPQAMKKMIPALVSQFISLIKDTSLATIIVLPDLMHNAQIVY 180

Query: 194 SVNRNYLAALF-VVALIMIVLNFSLTALASRIERQL 228
             N  Y+  +F ++A++  ++ ++L+ L+  +ER++
Sbjct: 181 GQNSTYILPMFLMIAIMYFIVCYALSVLSRSLERRM 216


Lambda     K      H
   0.323    0.136    0.395 

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: 153
Number of extensions: 9
Number of successful extensions: 2
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: 273
Length of database: 217
Length adjustment: 23
Effective length of query: 250
Effective length of database: 194
Effective search space:    48500
Effective search space used:    48500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 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