Alignments for a candidate for rhaT' in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Trichormus variabilis ATCC 29413

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_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  387 bits (995), Expect = e-112
 Identities = 218/505 (43%), Positives = 331/505 (65%), Gaps = 10/505 (1%)

Query: 12  SKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYR 71
           S    A  +LEM+GI++ F GV AL  V++ ++PG V AL+GENGAGKSTL+KIL G Y 
Sbjct: 10  SPPATATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYI 69

Query: 72  PNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDW 131
            +EGEI ++G+         A  AG+  I+QE  +   LTV ENIF+G +  TR + +D 
Sbjct: 70  ADEGEIRINGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMG-SELTRGQFLDR 128

Query: 132 QTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRK 191
           + M   ++ +L +L ++  PT  +  L+IA++  V IARAL   +RI++MDEPTAALS +
Sbjct: 129 KAMELEAQQVLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDR 188

Query: 192 EIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRK--TPQDE 249
           E + LF ++R L+  G AI++ISH+ +E+Y +AD   V   R  + +  ++R+  +PQ  
Sbjct: 189 ETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVL--RDGQYIGSLTREEISPQ-R 245

Query: 250 IVRMMVGRDVENVFPKIDVAIGGPV-LEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAG 308
           +V+MMVGR +++ +     +  GPV LE+RN S   + +  SF LR GEILG+ GL+GAG
Sbjct: 246 LVQMMVGRSMQDFYEHQRQSNPGPVVLEVRNISDGRKVQPASFQLRAGEILGLAGLVGAG 305

Query: 309 RSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQN 368
           R+E+S+ +FG  + +SG++ L G+++ IHSP DAI  GI YVPE+R   GL L M   +N
Sbjct: 306 RTEVSRLIFGADRKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMSSRKN 365

Query: 369 MTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428
           + L  L + +  G +   +   +A    E   +R A L +    LSGGNQQK+++ +WLA
Sbjct: 366 IGLNRLKQDANLGIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQKLLLARWLA 425

Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEG 488
             P+V++LDEPT+G+DIG+K+ ++  IS+L+A+G++I+MVSSELPEI+G+SDRVLVM+EG
Sbjct: 426 INPRVLMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLVMREG 485

Query: 489 LSAGIFERA---ELSPEALVRAATG 510
              G  + +   E++ E ++  ATG
Sbjct: 486 QLVGELDNSIGKEITQENIMHYATG 510



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 71/249 (28%), Positives = 126/249 (50%), Gaps = 12/249 (4%)

Query: 269 AIGGPVLEIRNYSHRTE----FRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLS 324
           A   PVLE++  + R       + ++ T+  GE+  + G  GAG+S L + L G      
Sbjct: 13  ATATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADE 72

Query: 325 GKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFL- 383
           G++ + G+ + I  P  A +AGI  + +E     +A  + + +N+ + S    +R  FL 
Sbjct: 73  GEIRINGKGVKITDPGTARQAGINLIYQELN---VAPNLTVTENIFMGS--ELTRGQFLD 127

Query: 384 RAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGI 443
           R A E   A++    L    A   + VGTL+   QQ+V I + L    +++++DEPT  +
Sbjct: 128 RKAMELE-AQQVLASLGASFAPTDI-VGTLAIAEQQQVEIARALKDNSRILVMDEPTAAL 185

Query: 444 DIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEA 503
                  +   I +L  +G++II +S  + EI  ++DR+ V+++G   G   R E+SP+ 
Sbjct: 186 SDRETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQR 245

Query: 504 LVRAATGNA 512
           LV+   G +
Sbjct: 246 LVQMMVGRS 254


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: 28
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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 Apr 09 2024. 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 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