Alignments for a candidate for rhaT' in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Rhodobacter viridis JA737

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_110805879.1 C8J30_RS10885 sugar ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_003217355.1:WP_110805879.1
          Length = 511

 Score =  327 bits (837), Expect = 8e-94
 Identities = 202/506 (39%), Positives = 291/506 (57%), Gaps = 19/506 (3%)

Query: 18  PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEI 77
           P  L +RG  +++PG +AL  V   L  G V  L+GENGAGKSTL+K++ G+    EG I
Sbjct: 6   PIGLSIRGGVKVYPGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDMTEGTI 65

Query: 78  LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137
            +DGR   F +   A+ AG+  + QE  LF  L+VAENIF+GH        ID +     
Sbjct: 66  TMDGREMRFRTKADAVAAGIGIVFQELNLFPNLSVAENIFIGHETTRGGIDIDIEAHREA 125

Query: 138 SKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197
           ++ L+  LE NI P   L +L I Q+ +V IA+AL+  ARI+I+DEPT+ALS  E++ LF
Sbjct: 126 TRQLMERLEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEVLF 185

Query: 198 RIVRGLKEQGKAILFISHKFDELYEIADDFVVFPR---RSRRPVRGVSRKTPQDEIVRMM 254
           R++  L  QG  I++ISH+ +EL  + D   V         R + GV        IV+ M
Sbjct: 186 RVIDELTAQGVGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVDIPW----IVKAM 241

Query: 255 VGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFR--------DISFTLRKGEILGVYGLIG 306
           +G   +  + + +VA  GP  EI      T  R         +S ++R GEI+G+YGL+G
Sbjct: 242 IGSSSKE-YGRSEVANFGP--EIFRAEDITLPRAGGGFTVDHVSLSIRSGEIVGLYGLMG 298

Query: 307 AGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIF 366
           AGRSE  + +        GK  +EG+ +T       I  GI  +PE+R R GL   M I 
Sbjct: 299 AGRSEFLECVMAQHPHSGGKFWVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIR 358

Query: 367 QNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 426
           +N+TL SL   ++   L    E   A ++ +RL ++ A+   PV +LSGGNQQKVVIGK 
Sbjct: 359 ENLTLSSLPSFTKLFHLDLKKEAKTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVIGKA 418

Query: 427 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 486
           L T PKV+++DEP++GIDIG+KA V   +  LAAEGL I+ V+S+L E++ +SDR++VM 
Sbjct: 419 LMTGPKVLLMDEPSRGIDIGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMA 478

Query: 487 EGLSAGIFERAELSPEALVRAATGNA 512
           +G   G F     + + ++ A T NA
Sbjct: 479 QGRVTGEFPSGTEAAK-VISATTPNA 503


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: 636
Number of extensions: 33
Number of successful extensions: 6
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: 511
Length adjustment: 35
Effective length of query: 477
Effective length of database: 476
Effective search space:   227052
Effective search space used:   227052
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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