Alignments for a candidate for rhaT' in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Herbaspirillum seropedicae SmR1

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 HSERO_RS05195 HSERO_RS05195 xylose ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__HerbieS:HSERO_RS05195
          Length = 518

 Score =  372 bits (954), Expect = e-107
 Identities = 206/505 (40%), Positives = 319/505 (63%), Gaps = 15/505 (2%)

Query: 20  ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNE--GEI 77
           ILEMRGI + FPGVKAL+NV++A+  G + A++GENGAGKSTL+K+L+G+Y      G+I
Sbjct: 4   ILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGDI 63

Query: 78  LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137
           +  G    F   + +   G+  IHQE  L   L+V EN+FLG+  + R   IDW+    R
Sbjct: 64  VYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNE-QARGGVIDWEQSYVR 122

Query: 138 SKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197
           +K LL  +     P  ++ DL + ++ L+ IA+ALS E +++I+DEPTA+L+  + D L 
Sbjct: 123 AKELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDALL 182

Query: 198 RIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTP--QDEIVRMMV 255
            ++  LK QG A + ISHK +E+ ++AD   V  R          R  P  +D I++ MV
Sbjct: 183 ELLLELKRQGIASILISHKLNEISKVADSITVL-RDGTTVDTFDCRAEPISEDRIIQHMV 241

Query: 256 GRDVENVFPKIDVAIGGPVLEIRNY-------SHRTEFRDISFTLRKGEILGVYGLIGAG 308
           GR++ + +P+ D  IG  + E+R++       + R   +D++ ++R GEI+G+ GL+GAG
Sbjct: 242 GREMADRYPQRDPQIGEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGAG 301

Query: 309 RSELSQSLFGIT--KPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIF 366
           R+EL++S+FG    K ++G+  L G+E+ + + + AI  GI YV E+R   GL L   I 
Sbjct: 302 RTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKAIAKGIAYVTEDRKGDGLVLEEDIK 361

Query: 367 QNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 426
           +N++L +L   S R  +  A E+ +A  + +++ +R +++   V  LSGGNQQKVV+ KW
Sbjct: 362 KNISLANLGGVSERTVIDEAREYKIAADFKQQMRIRCSSVLQKVVNLSGGNQQKVVLSKW 421

Query: 427 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 486
           L + P+V+ILDEPT+GID+G+K  ++  IS+LAAEG  IIM+SSE+PE++GM DR+ VM 
Sbjct: 422 LFSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELLGMCDRIYVMN 481

Query: 487 EGLSAGIFERAELSPEALVRAATGN 511
           EG   G   +AE + E ++RA   N
Sbjct: 482 EGQFVGHLPKAEATQENIMRAIMRN 506


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: 620
Number of extensions: 34
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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