GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Shewanella loihica PV-4

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= TCDB::Q88P35
         (384 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  193 bits (491), Expect = 5e-54
 Identities = 119/305 (39%), Positives = 185/305 (60%), Gaps = 18/305 (5%)

Query: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60
           M+TL +  V+  Y       L+ + L +  GE   L+GPSGCGK+TL+  IAGL+ I+ G
Sbjct: 1   MSTLTIEQVHSDYQG--QTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQG 58

Query: 61  AILIDEQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEV 116
            I I+ + +SG    +  + R++ M+FQ YAL+P ++V ENI FG+K   L +AA    +
Sbjct: 59  RISINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARL 116

Query: 117 ARVAKLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176
             +  L+++E L  R P +LSGGQQQRV++ RALA  P++ L DEP SN+DAK+R EM  
Sbjct: 117 GEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMV 176

Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFI 236
           E++ + ++   + V+VTH + EA    DK+A+ KDG I Q+G+ + +Y +P +++VA F+
Sbjct: 177 EIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236

Query: 237 GSPPMNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIAL-GA 295
           G   +N++   + +   RL  LL   Q+  +LP  +AA    G    L +RPEQ+ + G 
Sbjct: 237 GQ--VNYLSCEV-KDRARLQTLLGEVQSSSDLP--KAA----GYRGELLLRPEQLQMAGD 287

Query: 296 ADGNG 300
             G G
Sbjct: 288 EQGEG 292


Lambda     K      H
   0.320    0.137    0.391 

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: 293
Number of extensions: 10
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: 384
Length of database: 342
Length adjustment: 29
Effective length of query: 355
Effective length of database: 313
Effective search space:   111115
Effective search space used:   111115
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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