Alignments for a candidate for araVsh in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter related (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  353 bits (906), Expect = e-102
 Identities = 185/492 (37%), Positives = 308/492 (62%), Gaps = 7/492 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LE+  +SK +PGV AL DV LR+  G V AL+GENGAGKSTL+K++ G    D G++  
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRR-LGLIHFKKMYADAR 122
            G+P  F+TP+ A +AGI+ ++QE+NL+P++++A+N+++G E    L ++   +M+    
Sbjct: 86  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145

Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
            +L + ++ +D    + + SIA +Q++ IA+ V+  + +L++DEPT+++   EV  LF I
Sbjct: 146 RLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSI 205

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           +  LK++G  I++ITH +++V+ I+D + V R+G +IG      +    LI  M+GR L 
Sbjct: 206 IADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 265

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
           +    +++          ++LS+ D+S+ G  + ++  +  G+ +G+AGL+GSGR+ V  
Sbjct: 266 QLFPVREQP------IGELVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAE 319

Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362
           A+FG+     G I L GQ + +S P  AI  G AL  EDRK+ G+   LS+ EN+ +A+ 
Sbjct: 320 AIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 379

Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422
                  ++     + + +    KL++ TP  ++ I+ LSGGNQQK +LARWL   P +L
Sbjct: 380 PHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRIL 439

Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482
           +LDEPTRGID+GA AEI +LI  L  EGM++++ SSEL E++  S++V+V+ +   +  L
Sbjct: 440 ILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTL 499

Query: 483 SGAELTSQHVMQ 494
             +E T + VMQ
Sbjct: 500 DRSEATQERVMQ 511



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 62/248 (25%), Positives = 121/248 (48%), Gaps = 18/248 (7%)

Query: 3   LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62
           L+L ++ +S    G+   + VS  L AGE+  + G  G+G++ + + + G      G+I 
Sbjct: 278 LVLSVRDLS--LDGI--FKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIR 333

Query: 63  FLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPRRLG--LIHFKKM 117
             G+P   + P  A + G + + ++     L P L+V +N+ +   P  +G   I  K +
Sbjct: 334 LDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKAL 393

Query: 118 YADARAVLTQFKLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLD 172
               RA+       + V  P  +  I       QQ   +AR +  + ++L+LDEPT  +D
Sbjct: 394 ----RALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGID 449

Query: 173 AKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKL 232
                 ++ +++ L ++G+A++ I+  L +V  +SDR+ V+  G  +G    +E  Q ++
Sbjct: 450 VGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERV 509

Query: 233 IEAMLGRS 240
           ++   G S
Sbjct: 510 MQLASGLS 517


Lambda     K      H
   0.319    0.136    0.377 

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: 561
Number of extensions: 26
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: 499
Length of database: 517
Length adjustment: 34
Effective length of query: 465
Effective length of database: 483
Effective search space:   224595
Effective search space used:   224595
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: 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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Protein sequences (fasta format)
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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