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_523 Inositol transport system ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  469 bits (1208), Expect = e-137
 Identities = 242/491 (49%), Positives = 334/491 (68%), Gaps = 2/491 (0%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           LL++  + K FPGV ALS   L V PG V+AL+GENGAGKST+MK++ GIY  DAG L  
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            GK  TF  P ++ +AGI +IHQELNL+P ++IAENI++GRE +N    +D   M+    
Sbjct: 86  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
           +LL +L ++   ++ VG+LSI ++QMVEIAK +S++S ++IMDEPT A+T+TE   LF +
Sbjct: 146 RLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSI 205

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           I +LKSQG+GI+YI+H+M E+F I D+V VFRDG +I  +   S+  DSLI MMVGR+L 
Sbjct: 206 IADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 265

Query: 244 DQYPHLDKAPGDIRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302
             +P  ++  GD+ L V +L   G+   VSF L  GEILG++GLMG+GRT + + ++G  
Sbjct: 266 QLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVT 325

Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362
           P T G + LDG  V    P   +  G   ++EDRK  GL   +SV ENM +  L ++   
Sbjct: 326 PSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYV-G 384

Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422
            G ++    +    D  +   VKTPS+EQ I  LSGGNQQK  +AR LMT P++LILDEP
Sbjct: 385 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 444

Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482
           TRG+DVGAK EIY+LI+   ++G+++I++SSE+PEVLGMSDR++VMHEG L G   R +A
Sbjct: 445 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLNRGEA 504

Query: 483 TQEVLMAAAVG 493
           TQE +M  A G
Sbjct: 505 TQERVMQLASG 515



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 63/232 (27%), Positives = 109/232 (46%), Gaps = 9/232 (3%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   +DV   +R G +L + G  GAG++ LMK++ G     +G + L G  V   +P 
Sbjct: 37  PGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPL 96

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382
             L  GI  I ++     L+  MS+ EN+ +   R        + H +  +  +  +   
Sbjct: 97  AALQAGIAMIHQELN---LMPHMSIAENIWIG--REQLNGLHMVDHGEMHRCTARLLERL 151

Query: 383 NVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFK 442
            +K    EQ +G LS   +Q V IA+ +     +LI+DEPT  +       ++ +I   K
Sbjct: 152 RIKLDPEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSIIADLK 210

Query: 443 ADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           + G  II ++ +M EV  ++D + V  +G   G    +    + L++  VG+
Sbjct: 211 SQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR 262


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: 662
Number of extensions: 34
Number of successful extensions: 6
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: 517
Length adjustment: 34
Effective length of query: 467
Effective length of database: 483
Effective search space:   225561
Effective search space used:   225561
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:

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