Alignments for a candidate for fruK in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Pseudomonas putida KT2440

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  291 bits (744), Expect = 5e-83
 Identities = 168/458 (36%), Positives = 268/458 (58%), Gaps = 9/458 (1%)

Query: 23  LDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNA 82
           L  V L+L  GEV AL GENGAGKST+ K ++G+     G +   G+        +A+  
Sbjct: 31  LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERL 90

Query: 83  GIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDPHTPL 142
           G+  V QE+NL   L+V EN+ L +       I  K+  + A   +A++GL++IDP TP+
Sbjct: 91  GVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLATAAMARVGLDAIDPDTPV 150

Query: 143 SSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFVSH 202
             + I  QQ+V IAR ++ +  VLILDEPT+ L A EV  LF  + ++R  GVAI+++SH
Sbjct: 151 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYISH 210

Query: 203 FLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQIGAKKARREITP 262
            L+++  +  R+ +LR+G+ + +   +     EL+ +M+G+   E   +G    RR++  
Sbjct: 211 RLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLG----RRQL-- 264

Query: 263 GEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTL 322
              P++ V  L +   +  V  ++  GE+ G +GL+G+GRTEL RL+YGAD+ DSG   L
Sbjct: 265 -GAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIAL 323

Query: 323 N--GKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKE 380
               + V+I  P  A++  IA  TE+R+ EG++   ++  NI +           +  + 
Sbjct: 324 GQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEA 383

Query: 381 ADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGA 440
             A+ ++ ++ + +R A   + V  LSGGNQQKV+IGRWL    ++L+ DEPTRGID+GA
Sbjct: 384 EKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGA 443

Query: 441 KAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
           K +I  ++ +LA QG  +V +SS+L E++ + D I VL
Sbjct: 444 KFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVL 481



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 67/249 (26%), Positives = 118/249 (47%), Gaps = 15/249 (6%)

Query: 267 IVDVKGLGK---KGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLN 323
           ++   GLGK   +  +  V + +  GEV+   G  G+G++ L +L+ G + P +G  T  
Sbjct: 16  VLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYR 75

Query: 324 GKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADA 383
           G+         A +  +    +   +  ++  LTV +N+ +    +R  F  I  K    
Sbjct: 76  GQAYAPGSRGEAERLGVRMVMQ---ELNLLPTLTVAENLFLDNLPSR--FGWISHKRLRQ 130

Query: 384 IVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAE 443
           +    M  + +   DPD PV  L  G+QQ V I R L     +LILDEPT  +     A 
Sbjct: 131 LATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVAL 190

Query: 444 IQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIA 503
           +   +  L ++G+ +V+IS  LEE+ R++  I VL+D     ++  D+ + + +  E + 
Sbjct: 191 LFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRD----GKLVCDEPIQRYSSAELV- 245

Query: 504 NTNVNTGKE 512
             N+  G+E
Sbjct: 246 --NLMVGRE 252



 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 54/221 (24%), Positives = 104/221 (47%), Gaps = 11/221 (4%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ--QFNGTLDAQNAG 83
           V   +  GE+  + G  GAG++ +++ + G  + ++G I +   PQ    +    A  AG
Sbjct: 283 VSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAG 342

Query: 84  IATVYQE---VNLCTNLSVGENVMLGH----EKRGPFGIDWKKTHEAAKKYLAQMGLESI 136
           IA + ++     L    S+  N+ LG+     + G    + +K    A++ +  M + S 
Sbjct: 343 IALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKA--LAERQIQAMRIRSA 400

Query: 137 DPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVA 196
                +  +S   QQ V I R +  + +VL+ DEPT  +D     D++ ++ ++   G A
Sbjct: 401 GAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKA 460

Query: 197 ILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
           ++ VS  L ++  I DR+ +L  G+ I         +D+L+
Sbjct: 461 LVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLL 501


Lambda     K      H
   0.316    0.135    0.376 

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: 609
Number of extensions: 32
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 513
Length of database: 524
Length adjustment: 35
Effective length of query: 478
Effective length of database: 489
Effective search space:   233742
Effective search space used:   233742
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources