GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluD in Shewanella oneidensis MR-1

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate 200226 SO1043 amino acid ABC transporter, permease protein (NCBI ptt file)

Query= TCDB::P48245
         (273 letters)



>FitnessBrowser__MR1:200226
          Length = 226

 Score =  105 bits (263), Expect = 7e-28
 Identities = 67/204 (32%), Positives = 116/204 (56%), Gaps = 4/204 (1%)

Query: 26  ILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFA 85
           IL GL  TL    F+++L  V+G    L ++S    +R+   + +   R  PV++ ++  
Sbjct: 24  ILNGLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYIRFPAELYVGVIRGTPVVVQLVIL 83

Query: 86  YQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQ 145
           Y  F     +   ++  A + FGL   +G+ I+EI+R+GI ++ KGQ EAA +LG+S   
Sbjct: 84  Y--FIVLAALDVDKITAAIIAFGLN--SGAYISEIIRAGIQAVDKGQTEAARSLGLSQAM 139

Query: 146 TTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLAALFV 205
           T   I+LPQA+  +LPAL ++ ++ LK++A+   IG ++++R+G    S        LF 
Sbjct: 140 TMKLIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRAGEIIRSRTFEDSVPLFT 199

Query: 206 VALIMIVLNFSLTALASRIERQLR 229
            ALI + L +S T + S+ E++L+
Sbjct: 200 CALIYLFLTYSFTFMLSKFEKRLK 223


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: 150
Number of extensions: 14
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: 226
Length adjustment: 24
Effective length of query: 249
Effective length of database: 202
Effective search space:    50298
Effective search space used:    50298
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 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