GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pseudovibrio axinellae Ad2

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_068002943.1 PsAD2_RS04510 ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_001623255.1:WP_068002943.1
          Length = 363

 Score =  286 bits (731), Expect = 8e-82
 Identities = 149/296 (50%), Positives = 198/296 (66%), Gaps = 5/296 (1%)

Query: 25  NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84
           NLE+ + EF V VGPSGCGK+TTLRM+AGLE V+DG I+IGD+ V+ + P+ RD+AMVFQ
Sbjct: 23  NLEMEENEFTVFVGPSGCGKTTTLRMIAGLETVSDGEIYIGDRPVSQLEPKARDLAMVFQ 82

Query: 85  NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144
           +YALYPHM V +NM FAL++  + + EI+++V   A  LGLT+FL RKP  LSGGQRQRV
Sbjct: 83  DYALYPHMNVAKNMSFALRLQRRPRKEIDEKVGLVAEMLGLTKFLHRKPGELSGGQRQRV 142

Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204
           AMGRA+ R+   FL DEPLSNLDAKLR Q R ++A +++K+    +YVTHDQ EA+T+GD
Sbjct: 143 AMGRALARDAGTFLFDEPLSNLDAKLRCQMRAELAIMRQKVRKNMIYVTHDQIEAMTLGD 202

Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDA---TSGHA-RI 260
           RI V+  GY+QQ G P EL+ +PAN FVAGF+GSP MN     ++D       SG    +
Sbjct: 203 RIVVMNGGYIQQQGTPEELFKQPANKFVAGFLGSPPMNFLGAKIQDLGGQVFVSGDGFEV 262

Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFL 316
            L  E  +         + +G RP  L   P     + +I +K+   E +G+ S L
Sbjct: 263 ALPEERASVALGHSASSVILGIRPSDLHFSPHAPDHE-AIDLKVIVSEYIGAQSVL 317


Lambda     K      H
   0.316    0.135    0.380 

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: 389
Number of extensions: 15
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: 376
Length of database: 363
Length adjustment: 30
Effective length of query: 346
Effective length of database: 333
Effective search space:   115218
Effective search space used:   115218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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