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_110806166.1 C8J30_RS12430 ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_003217355.1:WP_110806166.1
          Length = 530

 Score =  286 bits (732), Expect = 1e-81
 Identities = 181/489 (37%), Positives = 272/489 (55%), Gaps = 17/489 (3%)

Query: 18  PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEI 77
           P  +E+RGIS+ F  V+A  ++SI + PGT+  ++GENGAGKSTL+ IL G YR + GEI
Sbjct: 19  PPAIELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEI 78

Query: 78  LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137
           L+DGRPT    +Q+AI AG+  + Q   L    +V EN+ LG       R    +   + 
Sbjct: 79  LIDGRPTVIPDSQSAIRAGIGMVFQHFKLVPNFSVLENVILGAEDGALLRPSLAKARKTL 138

Query: 138 SKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197
           +  L    E ++DP   +++LS+  +  V I +AL   A I+I+DEPT  L+  E D LF
Sbjct: 139 AD-LARDYELDVDPDALVEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADHLF 197

Query: 198 RIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGR 257
           RI+RGLK QGK IL I+HK  E+ EI D+  V  RR        +  T  +++  +MVGR
Sbjct: 198 RILRGLKAQGKTILLITHKLREIMEITDEVSVM-RRGEMVATVTTADTSPEQLAELMVGR 256

Query: 258 DVENVFPKIDVAIGGPVLEIRNYSHRTE------FRDISFTLRKGEILGVYGLIGAGRSE 311
            V    PK     G  VL + +  H T+       + I+ T+R GEILG+ G+ G G+SE
Sbjct: 257 KVLLHVPKGPANPGREVLRVSDL-HVTDALGVERLKGINLTIRAGEILGIAGVAGNGQSE 315

Query: 312 LSQSLFGITK-PLSGKMVLEGQEITI----HSPQDAIRAGIVYVPEERGRHGLALPMPIF 366
           L Q L G  K  +SG + +EG +I       + Q   + GI +VPE+R   GL L    +
Sbjct: 316 LLQVLGGFAKGTVSGMIAVEGAQIPAAGKGATGQTRRQIGISHVPEDRHHLGLILDFAAW 375

Query: 367 QNMTLPSLARTSRRGFLRAANEFALARK---YAERLDLRAAALSVPVGTLSGGNQQKVVI 423
           +N+     +    +      +  A+ R      +R D+R    S+P  + SGGNQQK+V+
Sbjct: 376 ENIAFGYHSAPEYQANALFMDNDAILRDTEGKMDRFDVRPPDPSLPAKSFSGGNQQKIVL 435

Query: 424 GKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVL 483
            + +   P ++++ +PT+G+DIG+   +H  I EL   G ++++VS EL EI+ +SDR+ 
Sbjct: 436 AREIERNPVLLLVGQPTRGVDIGAIEFIHRRIVELRDAGAAVLLVSVELDEILSLSDRIA 495

Query: 484 VMKEGLSAG 492
           VM +G   G
Sbjct: 496 VMFDGQIMG 504



 Score = 92.4 bits (228), Expect = 4e-23
 Identities = 79/245 (32%), Positives = 121/245 (49%), Gaps = 16/245 (6%)

Query: 273 PVLEIRNYSHR----TEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328
           P +E+R  S         +DIS  +R G I G+ G  GAG+S L   L+G  +  +G+++
Sbjct: 20  PAIELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEIL 79

Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERGRHGLALP-MPIFQNMTLPSLARTSRRGFLRAAN 387
           ++G+   I   Q AIRAGI  V +    H   +P   + +N+ L +      R  L  A 
Sbjct: 80  IDGRPTVIPDSQSAIRAGIGMVFQ----HFKLVPNFSVLENVILGAEDGALLRPSLAKAR 135

Query: 388 EFA--LARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDI 445
           +    LAR Y   LD+   AL   V  LS G+QQ+V I K L     ++ILDEPT  +  
Sbjct: 136 KTLADLARDY--ELDVDPDAL---VEELSVGHQQRVEILKALYRHADILILDEPTGVLTP 190

Query: 446 GSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALV 505
                +   +  L A+G +I++++ +L EI+ ++D V VM+ G        A+ SPE L 
Sbjct: 191 DEADHLFRILRGLKAQGKTILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLA 250

Query: 506 RAATG 510
               G
Sbjct: 251 ELMVG 255


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: 639
Number of extensions: 38
Number of successful extensions: 11
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: 530
Length adjustment: 35
Effective length of query: 477
Effective length of database: 495
Effective search space:   236115
Effective search space used:   236115
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