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 SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>lcl|FitnessBrowser__Smeli:SM_b20673 SM_b20673 sugar uptake ABC
           transporter ATP-binding protein
          Length = 526

 Score =  370 bits (949), Expect = e-107
 Identities = 219/504 (43%), Positives = 309/504 (61%), Gaps = 21/504 (4%)

Query: 20  ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79
           IL    IS+ F GV AL +V   L  G + AL+GENGAGKSTL+K+L+G+Y   EG + V
Sbjct: 18  ILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAVRV 77

Query: 80  DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139
           DG    F++ + A  AG+  IHQE  L  EL VA+NIFLG         +D +     ++
Sbjct: 78  DGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKASLEAAR 137

Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199
            LL  L   +DP  R+  L + ++ LV IA+ALS+EARI+IMDEPT+ALS  E   LF+I
Sbjct: 138 GLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRLFKI 197

Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSR----RPVRGVSRKTPQDEIVRMMV 255
           +R L   G  I++ISH+ DE+ +++D   VF R  R    RP+ G+   T    I+  MV
Sbjct: 198 MRQLAADGVGIIYISHRIDEVMQLSDRVTVF-RDGRHVWARPMAGLDENT----IIAAMV 252

Query: 256 GRDVENVFPKIDVAIGG--PVLEIRNYS--------HRTEFRDISFTLRKGEILGVYGLI 305
           GR++ +   + D   GG  PVL +R+ S         R   + +SF +R GEILG+ GL+
Sbjct: 253 GRNLLDAHRR-DRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLL 311

Query: 306 GAGRSELSQSLFGITKPL-SGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMP 364
           GAGR+E+ +++F   + L  G++ L+G  + I SP+DA R G   V E+R   GL L   
Sbjct: 312 GAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHES 371

Query: 365 IFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIG 424
           I  N+ LP + R +R G      E ALA+   + L +R A      GTLSGGNQQKVVIG
Sbjct: 372 IRDNVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIG 431

Query: 425 KWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLV 484
           KWLAT P+V++LDEPT+GID+G+K  ++  I +LA +GL+I++VSSELPE++ ++DR+LV
Sbjct: 432 KWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILV 491

Query: 485 MKEGLSAGIFERAELSPEALVRAA 508
           M EG   G+  R E S E +++ A
Sbjct: 492 MAEGRQTGLISREEASEERIMQLA 515



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 68/227 (29%), Positives = 110/227 (48%), Gaps = 11/227 (4%)

Query: 287 RDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAG 346
           +D+ F LR GEI  + G  GAG+S L + L G+     G + ++G+ +   + +DA  AG
Sbjct: 35  KDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAVRVDGETVRFSNVRDAEAAG 94

Query: 347 IVYVPEERG---RHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRA 403
           I  + +E       G+A  + + +   +  L    R+  L AA    L  +    LD  A
Sbjct: 95  IAIIHQELNLVPELGVADNIFLGRERVIAGLF-VDRKASLEAAR--GLLNRLGIELDPEA 151

Query: 404 AALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGL 463
                 VG L  G QQ V I K L+   +++I+DEPT  +  G    +   + +LAA+G+
Sbjct: 152 R-----VGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRLFKIMRQLAADGV 206

Query: 464 SIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
            II +S  + E++ +SDRV V ++G        A L    ++ A  G
Sbjct: 207 GIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTIIAAMVG 253


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: 634
Number of extensions: 25
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: 526
Length adjustment: 35
Effective length of query: 477
Effective length of database: 491
Effective search space:   234207
Effective search space used:   234207
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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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:

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:

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:

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