GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Tatumella morbirosei LMG 23360

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_038022060.1 HA49_RS08470 sulfate/thiosulfate ABC transporter ATP-binding protein CysA

Query= TCDB::G3LHY9
         (356 letters)



>NCBI__GCF_000757425.2:WP_038022060.1
          Length = 362

 Score =  184 bits (466), Expect = 4e-51
 Identities = 109/307 (35%), Positives = 178/307 (57%), Gaps = 18/307 (5%)

Query: 4   ITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSH 63
           I +  I  ++G  P       L ++D + + G   ALLGPSG GKTTLL II+GL   + 
Sbjct: 3   INIHQINKSFGKTPV------LNDIDLDISSGEMVALLGPSGSGKTTLLRIIAGLEHQNS 56

Query: 64  GRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPL----RNRGVAEADVDRR 119
           GRI F  +DV++L  + R++  VFQ   ++  MTV+DN+AF L    R    ++AD+ ++
Sbjct: 57  GRISFRDRDVSHLHARDRHVGFVFQHYALFRHMTVFDNIAFGLTVLPRRERPSQADIRKK 116

Query: 120 VRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVL 179
           V ++LEM+ L+  A R    L+  QKQ+++L R L   D + +L DEP   +D  ++  L
Sbjct: 117 VLNLLEMVQLSHLAGRYPAQLSGGQKQRVALARALAV-DPHILLLDEPFGALDAQVRKEL 175

Query: 180 RSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGY 239
           R  L++LH++  FT V+VTHDQ EA+  A+++VVM  G + Q GTP +++++P+  FV  
Sbjct: 176 RRWLRQLHEELQFTSVFVTHDQEEAMEVADRIVVMSQGNVEQTGTPEQVWKQPASRFVLE 235

Query: 240 FIGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRP---EFIRLGREGMP 296
           F+G   +N +  ++ G+ ++V      L++ P   G  + +L +RP   +  R   E  P
Sbjct: 236 FLGE--INRLQGQLVGNKLQVAGHQWPLDFTPAVQG--EVDLFLRPWETDISRGQSEATP 291

Query: 297 ITISKVE 303
           + +  VE
Sbjct: 292 LPVKVVE 298


Lambda     K      H
   0.321    0.137    0.405 

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: 313
Number of extensions: 15
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: 356
Length of database: 362
Length adjustment: 29
Effective length of query: 327
Effective length of database: 333
Effective search space:   108891
Effective search space used:   108891
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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