GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas stutzeri RCH2

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__psRCH2:GFF3591
          Length = 369

 Score =  241 bits (614), Expect = 3e-68
 Identities = 120/239 (50%), Positives = 169/239 (70%), Gaps = 9/239 (3%)

Query: 14  GEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKG 73
           GE   VR+++L+++ GEF+ LLGPSG GKTT+L M+AG E P+ G+I +  + + +    
Sbjct: 22  GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRAINN---- 77

Query: 74  IFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELL 133
             VPP  RD+ MVFQ+YAL+PHMTV +N+AFPL +R + + +I +RV+    ++ L    
Sbjct: 78  --VPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEGFR 135

Query: 134 NRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTT 193
           NR P +LSGGQ+QRVAL RA+V +PQ+ LMDEPL  LD +LR +M+ E+K L  +LGVT 
Sbjct: 136 NRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVTV 195

Query: 194 IYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP---PMNFLD 249
           +YVTHDQ EA+TM DR+AV ++G +QQ+  P  +Y+KP NTFVA F+G     P + LD
Sbjct: 196 VYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGENNRLPAHLLD 254


Lambda     K      H
   0.323    0.142    0.406 

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: 367
Number of extensions: 15
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: 372
Length of database: 369
Length adjustment: 30
Effective length of query: 342
Effective length of database: 339
Effective search space:   115938
Effective search space used:   115938
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 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