Alignments for a candidate for HSERO_RS03640 in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Pseudomonas fluorescens GW456-L13

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          Length = 514

 Score =  375 bits (963), Expect = e-108
 Identities = 206/497 (41%), Positives = 305/497 (61%), Gaps = 9/497 (1%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           T  L+  GI K+F    AL ++     PG++HALMGENGAGKSTL+K+L G + P  G +
Sbjct: 13  TGSLRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGAL 72

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
            +  R +  +    S  +G+ +I+QEL + P ++VA N+F+G  L    GLI+ + +R +
Sbjct: 73  QIGERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLG-HLPASFGLINRSTLRQQ 131

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
             A L+ L       +  GRLS+ ++Q VEIA+AL   + ++  DEPT++LS RE ++L 
Sbjct: 132 ALACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM 191

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV-RDEIDSERIVQMMVGR 242
            ++ RLRDEG  ++Y+SHRM EV+ + + VTV +DG +V       ++  +++V  MVGR
Sbjct: 192 AIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGR 251

Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIR-PASFDVRAGEVLGFAGLVGAGRTEL 301
            + + Y ++       A     ++V  L G  +R P SF+V  GE+LG  GLVGAGRTEL
Sbjct: 252 DIQDIYDYRPRQRGAVA-----LKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTEL 306

Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361
            RLL G    S G + L G  + +  PR A+ AGI   PEDRK +G+    +VA N  ++
Sbjct: 307 LRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINIS 366

Query: 362 VASRHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420
               H+  G L+R       A   I+ L VK  +    +  LSGGNQQK +L RWL +  
Sbjct: 367 ARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPM 426

Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480
           KVL+LDEPTRG+DI AK+EIYQ++H LA++G+AV+V+SS+L EV+GI DR+LV+ EG + 
Sbjct: 427 KVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALR 486

Query: 481 GELAGAAITQENIMRLA 497
           GEL+     + N+++LA
Sbjct: 487 GELSREQANESNLLQLA 503



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 61/224 (27%), Positives = 116/224 (51%), Gaps = 6/224 (2%)

Query: 29  IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 88
           +  GEI  L G  GAG++ L+++LSG+     G++ L G  + LR P  + AAGI L  +
Sbjct: 287 VHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPE 346

Query: 89  EL---AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGF-GASDLAG 142
           +     + P  SVA N+ + +    +  G L+     +   +  ++ L      A+    
Sbjct: 347 DRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIM 406

Query: 143 RLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHR 202
            LS   QQ+  + R L    +++++DEPT  +      +++ ++  L  EG+A+I +S  
Sbjct: 407 YLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSD 466

Query: 203 MAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246
           + EV  ++DR+ VL +G+  GEL R++ +   ++Q+ + R  ++
Sbjct: 467 LMEVMGISDRILVLCEGALRGELSREQANESNLLQLALPRQRAD 510


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: 663
Number of extensions: 29
Number of successful extensions: 8
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: 521
Length of database: 514
Length adjustment: 35
Effective length of query: 486
Effective length of database: 479
Effective search space:   232794
Effective search space used:   232794
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