GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pseudomonas stutzeri RCH2

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  287 bits (734), Expect = 4e-82
 Identities = 162/324 (50%), Positives = 212/324 (65%), Gaps = 16/324 (4%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA+VT +D   SY G   P  +  +L+I DGEF+V VGPSGCGKST LR++AGLE++T G
Sbjct: 1   MASVTLRDICKSYDGT--PITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            + I ++ V  + P+DR + MVFQ+YALYPHMTV ENM F LK+A   + EI +RV+  A
Sbjct: 59  DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L L + LERKPK LSGGQRQRVA+GR +VR P+VFL DEPLSNLDA LRVQ R +IA 
Sbjct: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           L +++  T +YVTHDQ EA+T+ D+I VL  G + QVG P  LY  P N FVAGF+GSP 
Sbjct: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238

Query: 241 MNLGTFSVKDGDATSGHARIKLS---PETL----AAMTPEDNGRITIGFRPEALEIIPEG 293
           MN     V+   A+     I+L    P TL    +A++P D   +T+G RPE   ++P  
Sbjct: 239 MNF--VEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGD--PLTLGIRPEHF-VMP-- 291

Query: 294 ESTDLSIPIKLDFVEELGSDSFLY 317
           +  D +   ++   E LG  + LY
Sbjct: 292 DEADFTFHGQITVAERLGQYNLLY 315


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: 393
Number of extensions: 22
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: 371
Length adjustment: 30
Effective length of query: 346
Effective length of database: 341
Effective search space:   117986
Effective search space used:   117986
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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