GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Acidovorax sp. GW101-3H11

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2058
          Length = 360

 Score =  244 bits (623), Expect = 3e-69
 Identities = 126/274 (45%), Positives = 178/274 (64%), Gaps = 8/274 (2%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           VK  + E+  G    ++GPSGCGK+TTLRM+AGLE+ T G IFIG KDVT + P  R+++
Sbjct: 27  VKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGEIFIGGKDVTTLGPAQRNVS 86

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140
           M+FQ+YAL+PHM V EN+ + L+++G+ +++   +  EA   +GL  F +R P  LSGGQ
Sbjct: 87  MMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALRGVGLVGFDDRLPSELSGGQ 146

Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200
           +QRVA+ RA+V  P+V L DEPLSNLDA+LR + R +I ALQ++L +T  YVTHDQ EA+
Sbjct: 147 QQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRALQQRLSLTVAYVTHDQAEAM 206

Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260
            + D+I V+  G + Q G+PR LY+ P + FVAGF+G   +     +V D D T     +
Sbjct: 207 AVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEAML---FPAVADADGT-----V 258

Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGE 294
            L P  L       +G + +  RPEA  I  +GE
Sbjct: 259 ALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGE 292


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: 377
Number of extensions: 19
Number of successful extensions: 2
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: 360
Length adjustment: 30
Effective length of query: 346
Effective length of database: 330
Effective search space:   114180
Effective search space used:   114180
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 17 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