Alignments for a candidate for rhaT' in Rhizobium freirei PRF 81

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Rhizobium freirei PRF 81

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 WP_004127105.1 RHSP_RS28505 sugar ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_000359745.1:WP_004127105.1
          Length = 513

 Score =  409 bits (1051), Expect = e-118
 Identities = 213/494 (43%), Positives = 328/494 (66%), Gaps = 2/494 (0%)

Query: 16  DAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEG 75
           +A  +L   GI + FPGV ALD+VS  L  GTV AL+GENGAGKSTL+KIL GIY P++G
Sbjct: 19  NAAYLLSAEGIRKEFPGVLALDDVSFHLKRGTVHALMGENGAGKSTLMKILAGIYIPDQG 78

Query: 76  EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMN 135
           ++ + G      S   A++ G+  IHQE  L   +TVAENI++   P+ RF  +D   M 
Sbjct: 79  DVRLKGVEIRLKSPLDALENGIAMIHQELNLMPYMTVAENIWIRREPKNRFGFVDHTEMR 138

Query: 136 SRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDD 195
            +++ L   L  +IDP I++++LS+A R +V IA+A+S  + ++IMDEPT+AL+ +E+  
Sbjct: 139 RKTEELFHRLNISIDPEIQVRELSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVAH 198

Query: 196 LFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMV 255
           LF+I+R L+ QG  I++I+HK +EL+EIAD+F VF R  +      S    +D+I+RMMV
Sbjct: 199 LFQIIRDLRTQGIGIVYITHKMNELFEIADEFSVF-RDGKYIGTHASTDVTRDDIIRMMV 257

Query: 256 GRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQS 315
           GR++  +FPK +V IG  VL +++ S    F ++SF +R GEILGV GL+G+GRS ++++
Sbjct: 258 GREITQMFPKEEVPIGETVLSVKDLSLDGVFSNVSFDVRAGEILGVAGLVGSGRSNVAET 317

Query: 316 LFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSL- 374
           +FG+T   SG + L G+  TI SP DAIR  + ++ E+R   G  L + + +NM +  L 
Sbjct: 318 IFGVTPASSGTIQLFGKAATISSPADAIRHRMAFLTEDRKDTGCLLILSVLENMQVAVLH 377

Query: 375 ARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVI 434
            +  R GF++         + A++L ++   L   +  LSGGNQQK +IG+W+ T P+++
Sbjct: 378 DKFVRGGFVQEGPIEQACEEMAKKLRVKTPNLDERIENLSGGNQQKALIGRWMLTNPRIL 437

Query: 435 ILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIF 494
           ILDEPT+GID+G+KA +H  ++E+A  G+++IM+SSE+PE++GMSDR++VM EG   G  
Sbjct: 438 ILDEPTRGIDVGAKAEIHRLVTEMARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGFL 497

Query: 495 ERAELSPEALVRAA 508
           +RA+ +   ++  A
Sbjct: 498 DRADATQVKVMELA 511



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 61/223 (27%), Positives = 111/223 (49%), Gaps = 5/223 (2%)

Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347
           D+SF L++G +  + G  GAG+S L + L GI  P  G + L+G EI + SP DA+  GI
Sbjct: 41  DVSFHLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGDVRLKGVEIRLKSPLDALENGI 100

Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALS 407
             + +E     L   M + +N+ +    + +R GF+          +   RL++      
Sbjct: 101 AMIHQELN---LMPYMTVAENIWIRREPK-NRFGFVDHTEMRRKTEELFHRLNISIDP-E 155

Query: 408 VPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIM 467
           + V  LS  N+Q V I K ++    V+I+DEPT  +     A +   I +L  +G+ I+ 
Sbjct: 156 IQVRELSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVAHLFQIIRDLRTQGIGIVY 215

Query: 468 VSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           ++ ++ E+  ++D   V ++G   G     +++ + ++R   G
Sbjct: 216 ITHKMNELFEIADEFSVFRDGKYIGTHASTDVTRDDIIRMMVG 258


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: 608
Number of extensions: 32
Number of successful extensions: 7
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: 513
Length adjustment: 35
Effective length of query: 477
Effective length of database: 478
Effective search space:   228006
Effective search space used:   228006
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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