GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>NCBI__GCF_900115975.1:WP_092482139.1
          Length = 390

 Score =  159 bits (403), Expect = 1e-43
 Identities = 83/222 (37%), Positives = 132/222 (59%), Gaps = 6/222 (2%)

Query: 21  LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKD---- 76
           ++N   ++++GE  +++G SG GKSTL+ C+  L   + G I VD  +I     K     
Sbjct: 44  IRNASFQVEEGEVFVIMGLSGSGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKF 103

Query: 77  --RDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPG 134
               +AMVFQ + L    +V  N+ +GL+++K+P  E  E   +      +    ++ P 
Sbjct: 104 RQEKVAMVFQHFGLLSHRTVIGNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPN 163

Query: 135 QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTH 194
           +LSGG QQRV + RALA  P I L DEP S LD  +R +M+ E+  +  RLK T +++TH
Sbjct: 164 ELSGGMQQRVGLARALANDPDILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITH 223

Query: 195 DQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236
           D  EA  +GD+VAVMKDG+I+Q GTP+++  +P + ++ +F+
Sbjct: 224 DINEAFKIGDRVAVMKDGVIEQIGTPEELLASPESEYIENFV 265



 Score = 24.3 bits (51), Expect = 0.006
 Identities = 14/60 (23%), Positives = 25/60 (41%)

Query: 200 MTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALL 259
           +T+ D +  +K+    +     D Y      F+   I        PL +  +DG+LL L+
Sbjct: 321 VTIDDTIKAIKENKTLREILKHDYYTTDCEAFLQDLIPKATDTKYPLAVIDEDGKLLGLI 380


Lambda     K      H
   0.319    0.138    0.393 

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: 354
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 386
Length of database: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
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 (21.7 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