Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N2E2

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  368 bits (944), Expect = e-106
 Identities = 203/473 (42%), Positives = 305/473 (64%), Gaps = 22/473 (4%)

Query: 35  LVGENGAGKSTMMKVLTGIYTRDAG--TLLW----LGKETTFTGPKSSQEAGIGIIHQEL 88
           L+GENGAGKST++K+L G    DAG  +L +    LG+  T   P   QE GI  I+QE 
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDT---PIRRQEVGIITIYQEF 57

Query: 89  NLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADKLLAKLNLRFKSDKLVGDLSIGDQQ 148
           NLI  +++AEN++LGRE + R G +DWK M+++A  +L  L L      +V  LS+ +QQ
Sbjct: 58  NLIADMSVAENMYLGREPL-RHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQ 116

Query: 149 MVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRGIVYISHRMKEIFEIC 208
           MVEIAK L+  +K+IIMDEPT AL+  E + L  +I +LK++G  I+Y+SH++ E+   C
Sbjct: 117 MVEIAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACC 176

Query: 209 DDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLEDQYPHLDKAPGDIRLKVDNL----C 264
           D  T+FRDG +I   +V  ++ D ++ +MVGR +E     L  APG++ LKV ++     
Sbjct: 177 DRYTIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAA 236

Query: 265 GPGVN-------DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVV 317
           G G +       D+S  +R GEI+G +GL+GAGRTEL +V++GA     G + ++G +V 
Sbjct: 237 GGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVS 296

Query: 318 T-RSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVS 376
             +SP++G+A G+  + EDRK+    L  S++ NMSL +L    R G  +    E Q + 
Sbjct: 297 PFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQ 356

Query: 377 DFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQ 436
           D+ +   +K  +   AIG LSGGNQQKV +AR +  +PKVLI+DEPTRG+DVGAK E++Q
Sbjct: 357 DYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQ 416

Query: 437 LINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMA 489
           L+      G+++I++SSE+PEV+ +SDRI+   EG ++G  + ++AT+E+LMA
Sbjct: 417 LLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMA 469



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 57/256 (22%), Positives = 115/256 (44%), Gaps = 27/256 (10%)

Query: 2   EALLQLKGIDKAFPG------VKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYT 55
           E +L+++ + +   G         L   +++V  G ++   G  GAG++ + +V+ G   
Sbjct: 223 EVMLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADG 282

Query: 56  RDAGTLLWLGKETT-FTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREF-------- 106
            D G +   G++ + F  P+    AG+        L+P+    +  FL            
Sbjct: 283 CDEGMIYVNGRQVSPFKSPREGIAAGVA-------LVPEDRKQQACFLSHSIRWNMSLPS 335

Query: 107 ---VNRFGK-IDWKTMYAEADKLLAKLNLRFKSDKL-VGDLSIGDQQMVEIAKVLSFESK 161
              + R+G  ID +           +L ++  +D + +G LS G+QQ V +A+ ++ + K
Sbjct: 336 LGGLQRWGMFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPK 395

Query: 162 VIIMDEPTDALTDTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIA 221
           V+I+DEPT  +       + +++ ++   G  ++ IS  + E+  + D +  FR+GQ   
Sbjct: 396 VLIVDEPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITG 455

Query: 222 EREVASLTEDSLIEMM 237
                  TE+ L+  M
Sbjct: 456 IVSADEATEELLMARM 471


Lambda     K      H
   0.318    0.137    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: 663
Number of extensions: 49
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 501
Length of database: 485
Length adjustment: 34
Effective length of query: 467
Effective length of database: 451
Effective search space:   210617
Effective search space used:   210617
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 (21.7 bits)
S2: 52 (24.6 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:

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