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

GapMind for catabolism of small carbon sources

Aligments 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_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969
          Length = 514

 Score =  383 bits (984), Expect = e-111
 Identities = 207/494 (41%), Positives = 309/494 (62%), Gaps = 9/494 (1%)

Query: 7   LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66
           L+  GI KSF    AL+++     PG++HALMGENGAGKSTL+K+L G + P  G++ + 
Sbjct: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75

Query: 67  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126
            + +A +    S A+G+ +I+QEL + P ++VA N+F+G  L  R GL++   +R +   
Sbjct: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLG-HLPARFGLVNRGVLRQQALT 134

Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186
           +L+ L       +  GRLS+ ++Q VEIA+AL   + ++  DEPT++LS RE ++L  ++
Sbjct: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194

Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVR-DEIDSERIVQMMVGRSLS 245
            RLRDEG  ++Y+SHRM EV+ + + VTV +DG +V       E+  +++V  MVGR + 
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304
           + Y ++     D A     +QV+ L G G   P SF V  GE+LG  GLVGAGRTEL RL
Sbjct: 255 DIYDYRPRERGDVA-----LQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRL 309

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           L G + +  G ++L  + + +  PR A+ AG+   PEDRK +G+    +V  N  ++   
Sbjct: 310 LSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369

Query: 365 RHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
            H+ LG L+R     G A   I+ L VK       +  LSGGNQQK +L RWL +  KVL
Sbjct: 370 SHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVL 429

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483
           +LDEPTRG+DI AK+EIYQ++H LA+ G+AV+V+SS+L EV+GI DR+LV+ EG + GEL
Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489

Query: 484 AGAAITQENIMRLA 497
           +     + N+++LA
Sbjct: 490 SRDQANESNLLQLA 503



 Score = 91.3 bits (225), Expect = 8e-23
 Identities = 66/237 (27%), Positives = 122/237 (51%), Gaps = 20/237 (8%)

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

Query: 89  EL---AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGFGASDLAGR 143
           +     + P  SV  N+ + +    + LG L+     R   D  ++ L      +  AG+
Sbjct: 347 DRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKV---KTPTAGQ 403

Query: 144 ----LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYI 199
               LS   QQ+  + R L    +++++DEPT  +      +++ ++  L  +G+A+I +
Sbjct: 404 KIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVV 463

Query: 200 SHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQHQRIAPA 256
           S  + EV  ++DR+ VL +G+  GEL RD+ +   ++Q+ + R        QR+A A
Sbjct: 464 SSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR--------QRVADA 512


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: 664
Number of extensions: 31
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.

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, 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