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_7 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  279 bits (713), Expect = 2e-79
 Identities = 176/490 (35%), Positives = 271/490 (55%), Gaps = 26/490 (5%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P LQ+R I K +   LA   + LTI PGEIHAL+GENGAGKSTLMK++ GV   D GE++
Sbjct: 12  PRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVI 71

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANV--FMGSELRTRLGLIDHAAMRS 122
             G+ V+LR+P  +R  GI +++Q  ++   +SVA N+   MG+   T         +  
Sbjct: 72  WQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGT------PKQLEP 125

Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182
           +   V R+ G       L   LSI E+Q+VEI R L+   R++I+DEPT+ L+ +E + L
Sbjct: 126 KIREVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDL 185

Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242
           F  +RRL  EG +I++ISH++ EV AL    TVLR G   G  V  E   +++ ++MVG 
Sbjct: 186 FVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGE 245

Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALA-------GGKIRPASFDVRAGEVLGFAGLVG 295
           +      + ++   DA      + VR L+       G  +     +VR GE++G AG+ G
Sbjct: 246 AAELIADYPKVTGGDAC-----LDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAG 300

Query: 296 AGRTELARLLFGAD--PRSGGDILLEGR-PVHIDQPRAAMRAGIAYVPEDRKGQGLFLQM 352
            G+ EL  LL G    PR+    +  G+ PV   +P A  + G+A+VP +R G G   ++
Sbjct: 301 NGQDELLALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPEL 360

Query: 353 AVAANATMNVASRHTRL--GLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKV 410
           ++A NA +  A +H  +  GL++   +  +A   I+R  VK    + P   LSGGN QK 
Sbjct: 361 SLADNALL-TAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKF 419

Query: 411 LLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDR 470
           +L R +   P++L+   PT GVD+ A + I++ +  L   G A++VIS +L E+  I DR
Sbjct: 420 ILGREILQQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDR 479

Query: 471 VLVMREGMIT 480
           +  +  G ++
Sbjct: 480 LGALCGGRLS 489



 Score = 82.4 bits (202), Expect = 4e-20
 Identities = 58/215 (26%), Positives = 104/215 (48%), Gaps = 9/215 (4%)

Query: 282 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPE 341
           +  GE+    G  GAG++ L ++++G      G+++ +G+ V +  P  A   GI  V +
Sbjct: 36  IAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIGMVFQ 95

Query: 342 DRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGK 401
                 LF  ++VA N  + + +          + L    R   +R  + +  PE  V  
Sbjct: 96  HFS---LFETLSVAQNIALAMGA-----AAGTPKQLEPKIREVSRRYGMTL-EPERLVHS 146

Query: 402 LSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSEL 461
           LS G +Q+V + R L    ++LILDEPT  +      +++  + RLA++G +++ IS +L
Sbjct: 147 LSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSILFISHKL 206

Query: 462 PEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496
            EV  +C    V+R G + G    A  + + + RL
Sbjct: 207 GEVRALCHSATVLRGGRVAGHCVPAECSDQQLARL 241


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: 709
Number of extensions: 43
Number of successful extensions: 9
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: 521
Length adjustment: 35
Effective length of query: 486
Effective length of database: 486
Effective search space:   236196
Effective search space used:   236196
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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