Alignments for a candidate for HSERO_RS03640 in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Pseudomonas fluorescens FW300-N2E2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  434 bits (1115), Expect = e-126
 Identities = 227/494 (45%), Positives = 327/494 (66%), Gaps = 6/494 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL++  + K F   +ALSD+ L +RPG + ALMGENGAGKSTLMK+++G++ PD GE+ L
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G+PV    P A+  AGI +I+QEL + P++S+A N+++G E    L ++DH  M   T 
Sbjct: 86  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            +L +L       +  G LSIAE+Q VEIA+A+ + S I+IMDEPT+A++E E   LF++
Sbjct: 146 RLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSI 205

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +  L+ +G  IIYI+H+M EV+A+AD V V RDG+++G    D +D + ++ MMVGR LS
Sbjct: 206 IADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 265

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304
           + +  +     D      V+ VR L+  G  +  SFD+ AGE+LG AGL+G+GRT +A  
Sbjct: 266 QLFPVREQPIGD-----LVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEA 320

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           +FG  P +GG+ILL+G+PV I  P  A+  G A + EDRK  GLF  ++V  N  M V  
Sbjct: 321 IFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 380

Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424
            +   G ++ ++L  +     ++L VK    E  +  LSGGNQQK LLARWL   P++LI
Sbjct: 381 HYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILI 440

Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484
           LDEPTRG+D+ AK+EIY+L+  LAS+G+AV++ISSELPEV+G+ DRV+VM EG + G L 
Sbjct: 441 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLN 500

Query: 485 GAAITQENIMRLAT 498
               TQE +M+LA+
Sbjct: 501 RGEATQERVMQLAS 514



 Score =  104 bits (259), Expect = 9e-27
 Identities = 68/220 (30%), Positives = 116/220 (52%), Gaps = 5/220 (2%)

Query: 29  IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 88
           +  GEI  + G  G+G++ + + + GV     GEILLDG+PV + DP  +   G  L+ +
Sbjct: 298 LHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTE 357

Query: 89  ELAVA---PNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASDLA-GR 143
           +  ++   P +SV  N+ M         G I   A+R+  + + ++L     + +     
Sbjct: 358 DRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDT 417

Query: 144 LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRM 203
           LS   QQ+  +AR L+   RI+I+DEPT  +      +++ ++  L  EG+A+I IS  +
Sbjct: 418 LSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSEL 477

Query: 204 AEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
            EV  ++DRV V+ +G  +G L R E   ER++Q+  G S
Sbjct: 478 PEVLGMSDRVMVMHEGDLMGTLNRGEATQERVMQLASGLS 517


Lambda     K      H
   0.320    0.135    0.378 

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: 672
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 521
Length of database: 517
Length adjustment: 35
Effective length of query: 486
Effective length of database: 482
Effective search space:   234252
Effective search space used:   234252
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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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, or view the source code.

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