Alignments for a candidate for rhaT' in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Phaeobacter inhibens BS107

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__Phaeo:GFF385
          Length = 509

 Score =  272 bits (695), Expect = 2e-77
 Identities = 176/492 (35%), Positives = 266/492 (54%), Gaps = 25/492 (5%)

Query: 17  APAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGE 76
           APAI E++GIS+ F  V+A  ++SI + PGT+  +IGENGAGKSTL+ IL G Y+ ++GE
Sbjct: 3   APAI-ELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGE 61

Query: 77  ILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNS 136
           + + G+ T    +QAAI AG+  + Q   L +  TV ENI LG A               
Sbjct: 62  VWIHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILG-AEDGGLLKPSLSKARK 120

Query: 137 RSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDL 196
             K L    E N+DP  R+ ++ +  +  V I +AL  +A I+I+DEPT  L+  E D L
Sbjct: 121 SLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQL 180

Query: 197 FRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVG 256
           FRI+  L+ +GK I+ I+HK  E+ E  D   V  RR        + +T  + +  +MVG
Sbjct: 181 FRILDRLRAEGKTIILITHKLREIMEYTDTVSVM-RRGEMTATVKTAETSPEHLAELMVG 239

Query: 257 RDVENVFPKIDVAIGGPVLEIRNYSHRTE-----FRDISFTLRKGEILGVYGLIGAGRSE 311
           R V     K+    G P+LEI N S   E      ++I  T+R GEILG+ G+ G G+SE
Sbjct: 240 RKVLLRVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSE 299

Query: 312 LSQSLFGITKPLSGKMVLEGQEITIHSPQDAIR----AGIVYVPEERGRHGLALPMPIFQ 367
           L + L G+ +   G + L G  + +       R    A + +VPE+R R GL +    ++
Sbjct: 300 LMEVLGGMREG-QGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWE 358

Query: 368 NMTL-----PSLAR--TSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQK 420
           N+       P   R        LRA  E  +A     + D+R     +     SGGNQQK
Sbjct: 359 NVAFGYHHAPEYQRGLLMNNAALRADTEAKMA-----KFDVRPPDPWLAAKNFSGGNQQK 413

Query: 421 VVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSD 480
           +V+ + +   P+++++ +PT+G+DIG+   +H  I EL  +G +I++VS EL EI+ ++D
Sbjct: 414 IVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLAD 473

Query: 481 RVLVMKEGLSAG 492
           RV VM +G+  G
Sbjct: 474 RVAVMFDGMIMG 485



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 71/233 (30%), Positives = 106/233 (45%), Gaps = 24/233 (10%)

Query: 287 RDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAG 346
           +DIS  +  G I G+ G  GAG+S L   L+G  K   G++ + G+   I   Q AI AG
Sbjct: 22  KDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIHGKRTEIPDSQAAISAG 81

Query: 347 IVYVPEERGRHGLALPMPIFQNMTL---------PSLARTSRRGFLRAANEFALARKYAE 397
           I  V +      L     + +N+ L         PSL++ +R+     A E+ L      
Sbjct: 82  IGMVFQH---FKLVENFTVLENIILGAEDGGLLKPSLSK-ARKSLKDLAAEYELNVDPDA 137

Query: 398 RLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISE 457
           R+D            +  G QQ+V I K L     ++ILDEPT  +       +   +  
Sbjct: 138 RID-----------EIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILDR 186

Query: 458 LAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           L AEG +II+++ +L EI+  +D V VM+ G      + AE SPE L     G
Sbjct: 187 LRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVG 239


Lambda     K      H
   0.320    0.137    0.382 

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: 617
Number of extensions: 41
Number of successful extensions: 10
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: 512
Length of database: 509
Length adjustment: 35
Effective length of query: 477
Effective length of database: 474
Effective search space:   226098
Effective search space used:   226098
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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