GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Paucidesulfovibrio gracilis DSM 16080

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  235 bits (600), Expect = 1e-66
 Identities = 142/348 (40%), Positives = 205/348 (58%), Gaps = 10/348 (2%)

Query: 4   VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63
           V L+ L+KR+G    V   DL ++  E + L+GPSGCGK+T LRMIAGLE  + G I I 
Sbjct: 45  VRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIK 104

Query: 64  GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123
           GR++ND P   RN+ M+FQ+YAL+PH T+ EN+ F LK      EE++ +VA+A  ++ L
Sbjct: 105 GRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRL 164

Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183
             + +R  SQLSGGQ+QR+A+ RAIV +PDV L DEPLS LD KLR ++R EI  +  ++
Sbjct: 165 PGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQL 224

Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243
             T ++VTHDQ EA+++S++IV+M+DG  +Q GTPEDV+  P   FVA F+G    N  +
Sbjct: 225 NLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFD 282

Query: 244 A----VLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAV 299
           A    VL + ++       L          R+GQ V   +R   +  +   L   + ++ 
Sbjct: 283 ARVLEVLDNDQVRVRIAEGLEFTADHVGRWRQGQDVHLVMRAQKINVTSPDLADEELEST 342

Query: 300 HEIELPVTITEP--LGNETLVFTQF-NG-RDWVSRMLNPRPLRPGEAV 343
                P  I +   +G ET  F +  NG R  +  M+  RP R G+ V
Sbjct: 343 DLNYYPGKIYDRSYMGGETSYFVELANGVRLHIISMVRRRPHRIGDEV 390


Lambda     K      H
   0.320    0.137    0.397 

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: 359
Number of extensions: 14
Number of successful extensions: 1
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: 365
Length of database: 406
Length adjustment: 30
Effective length of query: 335
Effective length of database: 376
Effective search space:   125960
Effective search space used:   125960
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: 50 (23.9 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