Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N1B4

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          Length = 526

 Score =  471 bits (1212), Expect = e-137
 Identities = 244/491 (49%), Positives = 332/491 (67%), Gaps = 2/491 (0%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           LL++  + K FPGV ALS   L V PG V+AL+GENGAGKST+MK++ GIY  DAG L  
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            GK   F  P ++ +AGI +IHQELNL+P ++IAENI++GRE +N    ID + M+    
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
           KLL +L +    ++LVG+LSI ++QMVEIAK +S++S ++IMDEPT A+TD E   LF +
Sbjct: 152 KLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 211

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           I +LK QG+GI+YI+H+M E+F I D+V VFRDG +I  +   S+  DSLI MMVGR+L 
Sbjct: 212 IADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 271

Query: 244 DQYPHLDKAPGDIRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302
             +P  +K  GD+ L V +L   G+  DVSF L  GEILG++GLMG+GRT + + ++G  
Sbjct: 272 QLFPVREKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 331

Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362
           P   G + LDG  V    P   +  G   ++EDRK  GL   +SV ENM +  L ++   
Sbjct: 332 PSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYV-G 390

Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422
            G ++    +    D  +   VKTPS+EQ I  LSGGNQQK  +AR LMT P++LILDEP
Sbjct: 391 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 450

Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482
           TRG+DVGAK EIY+LI+   ++G+++I++SSE+PEVLGMSDR++VMHEG L G   R +A
Sbjct: 451 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 510

Query: 483 TQEVLMAAAVG 493
           TQE +M  A G
Sbjct: 511 TQERVMQLASG 521



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 62/232 (26%), Positives = 108/232 (46%), Gaps = 9/232 (3%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   +DV   +R G +L + G  GAG++ LMK++ G     +G + L G  VV  +P 
Sbjct: 43  PGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVVFETPL 102

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382
             L  GI  I ++     L+  MS+ EN+ +   R        + H +  +  +  +   
Sbjct: 103 AALQAGIAMIHQELN---LMPHMSIAENIWIG--REQLNGLHMIDHREMHRCTAKLLERL 157

Query: 383 NVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFK 442
            +     E+ +G LS   +Q V IA+ +     +LI+DEPT  +       ++ +I   K
Sbjct: 158 RINLDP-EELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLK 216

Query: 443 ADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
             G  II ++ +M EV  ++D + V  +G   G    +    + L++  VG+
Sbjct: 217 RQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR 268


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: 665
Number of extensions: 34
Number of successful extensions: 7
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: 526
Length adjustment: 35
Effective length of query: 466
Effective length of database: 491
Effective search space:   228806
Effective search space used:   228806
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