GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Lactobacillus shenzhenensis LY-73

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_022529220.1 L248_RS05900 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000469325.1:WP_022529220.1
          Length = 516

 Score =  312 bits (799), Expect = 2e-89
 Identities = 180/502 (35%), Positives = 292/502 (58%), Gaps = 17/502 (3%)

Query: 17  SSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS 76
           S S   I +R + KRF   +A D+   ++ +GEVH L+GENGAGK+T+M +LSG+ Q  S
Sbjct: 2   SQSDIAIEVRGLTKRFGDFVANDHISMQIRSGEVHGLLGENGAGKTTMMNMLSGILQPTS 61

Query: 77  GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDE 136
           G+IL+ G+PV +   + A  LGIG++HQ   L+ + +  +NI +G E  K +G+      
Sbjct: 62  GEILVHGQPVHLASAKDATRLGIGMVHQHFMLVENFTVLENIMLGVEETKGLGV------ 115

Query: 137 LNRQAA-----AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAAL 191
           LNR+AA     A+  +  L +DP   VG+++V  QQ  EI K L  ++ +LI DEPTA L
Sbjct: 116 LNRRAARDKVMALSKQYGLAVDPDAKVGDISVGMQQRAEILKVLYRNADILIFDEPTAVL 175

Query: 192 NNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDT 251
              EI EL  I + L  +G  ++ ISHK++EL+ +A   +++R GK I TV  + TS + 
Sbjct: 176 TPQEIKELLAIFQRLAQEGKAVILISHKLNELQAVAKVTTIIRRGKVIDTVDTKATSTEK 235

Query: 252 IISMMVGRALDGEQRIPPDTSRNDVV----LEVRGLNRGRAIRDVSFTLRKGEILGFAGL 307
           +  +MVGR +  ++   P  +  +++    L+V    +   + D   T+  GEI+G AG+
Sbjct: 236 LAELMVGRHVTFQRDRVPMPAGPEILKISHLQVVDNQKVTRVHDFDLTIHGGEIVGLAGI 295

Query: 308 MGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367
            G G++E+ RAI G  P   G++ I G      +P      G+G++ EDR+ +GL + M 
Sbjct: 296 DGNGQSELVRAITGLMPTAGGQVTIAGQDRTGATPRQITRSGVGHIPEDRQRYGLILPMS 355

Query: 368 VQANIALS--SMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIV 425
           +  N++L   ++  ++  G ++Q+A+    +  + Q  ++  S+ + A  LSGGNQQK++
Sbjct: 356 LVDNMSLQVYTVAPYSHHGVLNQKAMVTTTEQLLDQYDVRHSSIMEPAGALSGGNQQKLI 415

Query: 426 IAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRV 485
           IA+ L R+  +L    PTRG+DVGA   I+  L A    G AI++IS EL E+ ++S RV
Sbjct: 416 IARELSREPQLLIAVNPTRGLDVGAIEFIHSQLLAARAAGHAILLISYELDEIRQLSDRV 475

Query: 486 LVMCEGRITGELARADATQEKI 507
            V+ +G I G+   +D ++ +I
Sbjct: 476 AVIHQGTIVGQAKTSDLSESEI 497



 Score =  107 bits (268), Expect = 8e-28
 Identities = 75/249 (30%), Positives = 129/249 (51%), Gaps = 13/249 (5%)

Query: 272 SRNDVVLEVRGLNR--GRAIRD--VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA 327
           S++D+ +EVRGL +  G  + +  +S  +R GE+ G  G  GAG+T +   + G     +
Sbjct: 2   SQSDIAIEVRGLTKRFGDFVANDHISMQIRSGEVHGLLGENGAGKTTMMNMLSGILQPTS 61

Query: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMD 387
           GEI++HG    + S  DA   GIG + +   HF L     V  NI L  +     +G ++
Sbjct: 62  GEILVHGQPVHLASAKDATRLGIGMVHQ---HFMLVENFTVLENIMLG-VEETKGLGVLN 117

Query: 388 QRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRG 445
           +RA R+      +Q  +   +V+  A++  +S G QQ+  I K L R+ DIL FDEPT  
Sbjct: 118 RRAARDKVMALSKQYGL---AVDPDAKVGDISVGMQQRAEILKVLYRNADILIFDEPTAV 174

Query: 446 IDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQE 505
           +      E+  +   LA++GKA+++IS +L E+  ++    ++  G++   +     + E
Sbjct: 175 LTPQEIKELLAIFQRLAQEGKAVILISHKLNELQAVAKVTTIIRRGKVIDTVDTKATSTE 234

Query: 506 KIMQLATQR 514
           K+ +L   R
Sbjct: 235 KLAELMVGR 243



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 60/229 (26%), Positives = 106/229 (46%), Gaps = 12/229 (5%)

Query: 48  GEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII---HQ 104
           GE+  L G +G G+S L++ ++G+     G + + G+      PRQ    G+G I    Q
Sbjct: 287 GEIVGLAGIDGNGQSELVRAITGLMPTAGGQVTIAGQDRTGATPRQITRSGVGHIPEDRQ 346

Query: 105 ELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM------DPSTPV 158
              L+  +S   N+ +       +  +     LN++A        LD           P 
Sbjct: 347 RYGLILPMSLVDNMSL---QVYTVAPYSHHGVLNQKAMVTTTEQLLDQYDVRHSSIMEPA 403

Query: 159 GELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISH 218
           G L+   QQ + IA+ LS + ++LI   PT  L+   I  +   +   +A G  I+ IS+
Sbjct: 404 GALSGGNQQKLIIARELSREPQLLIAVNPTRGLDVGAIEFIHSQLLAARAAGHAILLISY 463

Query: 219 KMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQRI 267
           ++DE+RQ++DRV+V+  G  +      + S   I  +M G  + G++ +
Sbjct: 464 ELDEIRQLSDRVAVIHQGTIVGQAKTSDLSESEIGLLMAGETVPGKEEM 512


Lambda     K      H
   0.320    0.135    0.372 

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: 619
Number of extensions: 35
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 520
Length of database: 516
Length adjustment: 35
Effective length of query: 485
Effective length of database: 481
Effective search space:   233285
Effective search space used:   233285
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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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:

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