GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas putida KT2440

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate PP_5168 PP_5168 sulfate/thiosulfate import ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__Putida:PP_5168
          Length = 329

 Score =  224 bits (571), Expect = 2e-63
 Identities = 132/324 (40%), Positives = 185/324 (57%), Gaps = 19/324 (5%)

Query: 3   ALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISI 62
           ++++ NV K F   + L  INL +  GE V  +GPSGCGK+TLLR+I+GLE    G I  
Sbjct: 2   SIEVRNVSKRFNSFQALNAINLDINSGELVALLGPSGCGKTTLLRIIAGLETPDQGNIVF 61

Query: 63  GGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALAL----KQERQPKEEIAARVAEAS 118
            G+ V+      R +  VFQ YAL+ H+SV +N+A  L    K ER  + +IA +V E  
Sbjct: 62  HGEDVSGHDVRDRNVGFVFQHYALFRHMSVFDNVAFGLRMKPKGERPSESKIAEKVHELL 121

Query: 119 RMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIAR 178
            M+ L+   DR P +LSGGQRQR+A+ RA+  EPK+ L DEP   LDA +R   R  +AR
Sbjct: 122 NMVQLDWLSDRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLAR 181

Query: 179 LHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPA 238
           LH  ++ + ++VTHDQ EAM +AD+IVV+  G IEQ+G+P E+Y+ PAN FV  F+G   
Sbjct: 182 LHEDINLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGSPGEVYDQPANDFVYHFLG--- 238

Query: 239 MNFVPAQRLGGNPGQFIGIRPEYARIS---PVGPLAGEVIHVEKLGGDTNILVDM-GEDL 294
                + RL  + G  +  RP    +S     G  A EV  +  LG  T + + + G+  
Sbjct: 239 ----DSNRLALSEGHHVLFRPHEVSLSRHETEGHHAAEVRDIRPLGATTRVTLKVEGQSE 294

Query: 295 TFTARLFGQHDTNV----GETLQF 314
              A +   HD+      GETL F
Sbjct: 295 LIEAEVVKDHDSLTGLARGETLFF 318


Lambda     K      H
   0.320    0.137    0.391 

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: 286
Number of extensions: 14
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: 331
Length of database: 329
Length adjustment: 28
Effective length of query: 303
Effective length of database: 301
Effective search space:    91203
Effective search space used:    91203
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 (21.8 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