Aligments for a candidate for HSERO_RS03640 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments 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 GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__WCS417:GFF2162
          Length = 500

 Score =  387 bits (995), Expect = e-112
 Identities = 210/499 (42%), Positives = 314/499 (62%), Gaps = 9/499 (1%)

Query: 7   LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66
           L+  GI K+F    AL  +  +  PG++HALMGENGAGKSTL+K+L G + P+ G + + 
Sbjct: 6   LRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLHIG 65

Query: 67  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126
            + +A +    S A+G+ +I+QEL + P +SVA N+F+G  L +R G+++   +R +  A
Sbjct: 66  EQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLG-HLPSRFGVVNRGLLRKQALA 124

Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186
            L+ L      ++  GRLS+ ++Q VEIA+AL   + ++  DEPT++LS RE ++L  ++
Sbjct: 125 CLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 184

Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV-RDEIDSERIVQMMVGRSLS 245
            RLRDEG  ++Y+SHRM EV+ + + VTV +DG +V        +  +++V  MVGR + 
Sbjct: 185 ARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRDIQ 244

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIR-PASFDVRAGEVLGFAGLVGAGRTELARL 304
           + Y ++     + A     ++V  L G  +R P SF+VR GE+LG  GLVGAGRTEL RL
Sbjct: 245 DIYDYRPREHGEVA-----LKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRL 299

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           L G +  S G + L G P+H+  PR A+ AG+   PEDRK +G+    +VA N  ++   
Sbjct: 300 LSGLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARG 359

Query: 365 RHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
            H+  G L+R     G A   I  + VK  +    +  LSGGNQQK +L RWL +  KVL
Sbjct: 360 AHSTFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVL 419

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483
           +LDEPTRG+DI AK+EIYQ++H LA+QG+AV+V+SS+L EV+GI DR+LV+ EG + GE 
Sbjct: 420 LLDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQ 479

Query: 484 AGAAITQENIMRLATDTNV 502
                T+ N+++LA   +V
Sbjct: 480 TREHATESNLLQLALPRSV 498



 Score = 91.3 bits (225), Expect = 8e-23
 Identities = 61/223 (27%), Positives = 114/223 (51%), Gaps = 6/223 (2%)

Query: 29  IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 88
           +R GEI  L G  GAG++ L ++LSG+     G++ L G P+ L+ P  + AAG+ L  +
Sbjct: 277 VRKGEILGLFGLVGAGRTELFRLLSGLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPE 336

Query: 89  EL---AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGF-GASDLAG 142
           +     + P  SVA N+ + +    +  G L+     +   D  +  +      A+    
Sbjct: 337 DRKKEGIIPLSSVAENINISARGAHSTFGWLLREGWEKGNADQQINAMKVKTPNAAQKIM 396

Query: 143 RLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHR 202
            LS   QQ+  + R L    +++++DEPT  +      +++ ++  L  +G+A+I +S  
Sbjct: 397 YLSGGNQQKSILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSD 456

Query: 203 MAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           + EV  +ADR+ VL +G+  GE  R+      ++Q+ + RS++
Sbjct: 457 LMEVMGIADRILVLCEGALRGEQTREHATESNLLQLALPRSVA 499


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: 661
Number of extensions: 25
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: 500
Length adjustment: 34
Effective length of query: 487
Effective length of database: 466
Effective search space:   226942
Effective search space used:   226942
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, 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