GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluD in Stutzerimonas stutzeri A1501

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease

Query= TCDB::P48245
         (273 letters)



>NCBI__GCF_000013785.1:WP_011913471.1
          Length = 222

 Score = 94.7 bits (234), Expect = 1e-24
 Identities = 64/207 (30%), Positives = 101/207 (48%), Gaps = 9/207 (4%)

Query: 25  YILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIF 84
           ++L G W T+  ++  +   L++G  L L R+     L+W   V +  FR  P+L+ +  
Sbjct: 15  FLLKGAWWTVVLSLSGMFFGLLLGFGLALLRLYAFWPLQWLARVYVSFFRGTPLLVQLFM 74

Query: 85  AYQMFAQYNIVPSSQL-AFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSS 143
            Y    Q  I    QL    A + G ++   +  AEILR+ IAS+ +GQ EAA ++GM  
Sbjct: 75  IYYGLPQLGI----QLDPLPAALIGFSLNMAAYTAEILRAAIASIDRGQWEAAASIGMGR 130

Query: 144 RQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSG----IQSASVNRNY 199
            QT +  +LPQA    LP L +  +  +KD+AL   I   E+ R       ++  +   Y
Sbjct: 131 AQTLYRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTFEIFTMY 190

Query: 200 LAALFVVALIMIVLNFSLTALASRIER 226
           LAA  +  L+  VL +    L  R+ R
Sbjct: 191 LAAALIYWLLASVLAYFQGRLEHRVNR 217


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: 155
Number of extensions: 6
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: 222
Length adjustment: 24
Effective length of query: 249
Effective length of database: 198
Effective search space:    49302
Effective search space used:    49302
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 Apr 09 2024. 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