Alignments for a candidate for HSERO_RS03640 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Pseudomonas simiae WCS417

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  427 bits (1097), Expect = e-124
 Identities = 223/494 (45%), Positives = 326/494 (65%), Gaps = 6/494 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL++  I K F   +AL+D+ L +RPG + ALMGENGAGKSTLMK+++G++ PD GEI L
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G+P+    P A++ AGI +I+QEL + P++S+A N+++G E    L +++H  M   T 
Sbjct: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            +L +L       +  G LSIAE+Q VEIA+A+ + S I+IMDEPT+A++E+E   LF++
Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +  L+ +G  I+YI+H+M EV+A+AD V V RDG ++G    D ++S+ ++ MMVGR LS
Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304
           + +  +     D      ++ VR L   G  +  SFD+ AGE+LG AGL+G+GRT +A  
Sbjct: 263 QLFPLRETPIGD-----LLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAET 317

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           +FG  P S G I L+G+ V I  P  A+  G A + EDRK  GLF  ++V  N  M V  
Sbjct: 318 IFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 377

Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424
            +T  G ++ ++L  +     ++L VK    E  +  LSGGNQQK LLARWL   P++LI
Sbjct: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437

Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484
           LDEPTRG+D+ AK+EIY+L+  LAS+G+AV++ISSELPEV+G+ DRV+VM EG + G L 
Sbjct: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497

Query: 485 GAAITQENIMRLAT 498
            +  TQE +M+LA+
Sbjct: 498 RSEATQEKVMQLAS 511



 Score =  100 bits (249), Expect = 1e-25
 Identities = 63/223 (28%), Positives = 116/223 (52%), Gaps = 5/223 (2%)

Query: 24  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83
           D+   +  GEI  + G  G+G++ + + + G+     G+I LDG+ V + DP  +   G 
Sbjct: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349

Query: 84  NLIYQELAVA---PNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASD 139
            L+ ++  ++   P +SV  N+ M      T  G I   A+R+  + + ++L     + +
Sbjct: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409

Query: 140 LA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 198
                LS   QQ+  +AR L+   R++I+DEPT  +      +++ ++  L  EG+A+I 
Sbjct: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469

Query: 199 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
           IS  + EV  ++DRV V+ +G  +G L R E   E+++Q+  G
Sbjct: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512



 Score = 97.8 bits (242), Expect = 8e-25
 Identities = 68/241 (28%), Positives = 119/241 (49%), Gaps = 10/241 (4%)

Query: 267 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHID 326
           V ALA  ++R     VR G VL   G  GAG++ L +++ G      G+I L G+P+  +
Sbjct: 36  VVALADVQLR-----VRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE 90

Query: 327 QPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQ 386
            P AA +AGIA + ++     L   M++A N  +     ++ L +V  R +       + 
Sbjct: 91  TPLAAQKAGIAMIHQELN---LMPHMSIAENIWIGREQLNS-LHMVNHREMHRCTAELLA 146

Query: 387 RLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHR 446
           RL + +  PE  VG LS   +Q V +A+ +     +LI+DEPT  +     + ++ ++  
Sbjct: 147 RLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIAD 205

Query: 447 LASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTA 506
           L SQG  +V I+ ++ EV  I D V V R+G   G     ++  ++++ +     + +  
Sbjct: 206 LKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLF 265

Query: 507 P 507
           P
Sbjct: 266 P 266


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: 615
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
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
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