GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Pseudomonas fluorescens FW300-N2C3

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  431 bits (1107), Expect = e-125
 Identities = 226/494 (45%), Positives = 328/494 (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
           + +    +      +L  V+ VR L+  G  +  SFD+ AGE+LG AGL+G+GRT +A  
Sbjct: 266 QLFP---VREQPIGEL--VLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEA 320

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           +FG  P +GG+I L+G+PV I  P  A+  G A + EDRK  GLF  ++V  N  M V  
Sbjct: 321 IFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 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 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLD 500

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



 Score =  102 bits (254), Expect = 3e-26
 Identities = 67/220 (30%), Positives = 115/220 (52%), Gaps = 5/220 (2%)

Query: 29  IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 88
           +  GEI  + G  G+G++ + + + GV     GEI LDG+PV + DP  +   G  L+ +
Sbjct: 298 LHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTE 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 PEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGLS 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: 662
Number of extensions: 23
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:

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