Aligments for a candidate for rhaT' in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for rhaT' in Sinorhizobium meliloti 1021

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 SMc02325 SMc02325 ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>lcl|FitnessBrowser__Smeli:SMc02325 SMc02325 ABC transporter
           ATP-binding protein
          Length = 503

 Score =  640 bits (1650), Expect = 0.0
 Identities = 333/493 (67%), Positives = 398/493 (80%), Gaps = 2/493 (0%)

Query: 18  PAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEI 77
           PAI  + GIS+ FPGV+AL +VS+AL+PG+VTAL+GENGAGKSTLVKILTGIY+P+ G I
Sbjct: 3   PAIA-LEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTI 61

Query: 78  LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137
            +    TTF +A AA  AGVTAIHQETVLFDEL+VAENIFLGHAPR RF  IDW+ +N+ 
Sbjct: 62  RLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNAD 121

Query: 138 SKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLF 197
           ++ALL    ++ DPTIRL+DL IA++HLVAIARALS++AR+VIMDEPTAALS KEI +L+
Sbjct: 122 AQALLGRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELY 181

Query: 198 RIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGR 257
            ++  LK  GKA+LFISHKFDE++ IAD + VF R       G+     QD++VRMMVGR
Sbjct: 182 DLIERLKADGKAVLFISHKFDEIFRIADRYTVF-RDGAMIGEGLIADVSQDDLVRMMVGR 240

Query: 258 DVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317
            V +V+PK +V IG PVL +  Y H TEF DI+F LR+GEILG YGL+GAGRSE  QSL 
Sbjct: 241 AVGSVYPKKEVTIGQPVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLI 300

Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377
           GIT+P +G + L+G+ + I SP +AIRAGIVYVPEERGR G  + MPIFQN+TLPSL+ T
Sbjct: 301 GITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHT 360

Query: 378 SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILD 437
           SR GFLR A EFALAR+Y  RLDLRAAAL   VGTLSGGNQQKVVI KWLAT PKVIILD
Sbjct: 361 SRSGFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIILD 420

Query: 438 EPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERA 497
           EPTKGIDIGSKAAVH F+SELAA+GLS+IMVSSE+PEI+GMSDRV+VM+EG  AG +ER+
Sbjct: 421 EPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERS 480

Query: 498 ELSPEALVRAATG 510
           EL+ E LVRAA G
Sbjct: 481 ELTAEKLVRAAAG 493



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 63/228 (27%), Positives = 109/228 (47%), Gaps = 11/228 (4%)

Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347
           D+S  L  G +  + G  GAG+S L + L GI +P +G + L   E T  +   A RAG+
Sbjct: 22  DVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRLGDTETTFPTALAASRAGV 81

Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAA-- 405
             + +E     L   + + +N+ L    R +R G +    ++      A+ L  RA A  
Sbjct: 82  TAIHQETV---LFDELSVAENIFLGHAPR-NRFGLI----DWKQLNADAQALLGRAGADF 133

Query: 406 -LSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLS 464
             ++ +  L    +  V I + L+   +V+I+DEPT  +       ++  I  L A+G +
Sbjct: 134 DPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYDLIERLKADGKA 193

Query: 465 IIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATGNA 512
           ++ +S +  EI  ++DR  V ++G   G    A++S + LVR   G A
Sbjct: 194 VLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGRA 241


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: 808
Number of extensions: 23
Number of successful extensions: 6
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: 503
Length adjustment: 34
Effective length of query: 478
Effective length of database: 469
Effective search space:   224182
Effective search space used:   224182
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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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, or view the source code.

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