GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Desulfacinum infernum DSM 9756

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  179 bits (454), Expect = 1e-49
 Identities = 111/327 (33%), Positives = 168/327 (51%), Gaps = 11/327 (3%)

Query: 2   LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61
           +E+R+  K  G    +      +E G L V+LGP+  GKT+L+RL+AGL+  T G+IH  
Sbjct: 3   IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62

Query: 62  GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121
           GTDVT +P  KRN++MV+Q +  +P L V  NI   +++    A  I+R +++  +LL L
Sbjct: 63  GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122

Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181
           +  LD  P  LSGG QQR AL RA++    + LMDEPL+NLD KLR  +R E+  +  + 
Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182

Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241
           G   +Y T +  EA+ +      +  G++ Q       Y RP N   A     PP+N + 
Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242

Query: 242 VTKS-GNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSE 300
           +  + G     P G  +       + PD        P +L LA ++G  A +  R    E
Sbjct: 243 LCPTQGGAALEPGGRLL----FPGMDPD-RYLFGIRPENLRLA-ESGQPAMVTGR----E 292

Query: 301 ITGSESFVHLEYDGVRWVMLAHGIHDI 327
             GS++FV  E  G   ++   G  +I
Sbjct: 293 YLGSDTFVSCEIHGQEVIVRTRGRRNI 319


Lambda     K      H
   0.319    0.136    0.392 

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: 322
Number of extensions: 13
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: 358
Length of database: 365
Length adjustment: 29
Effective length of query: 329
Effective length of database: 336
Effective search space:   110544
Effective search space used:   110544
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: 49 (23.5 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