GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Herbaspirillum seropedicae SmR1

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  429 bits (1102), Expect = e-124
 Identities = 225/496 (45%), Positives = 335/496 (67%), Gaps = 5/496 (1%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P++ ++++ KRFPGV AL     E   GEVHA++GENGAGKSTLMKI++GVYQ D G+I+
Sbjct: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKR--GIFIDYKKMYRE 120
            +G+ V    P +A   GI  + QEL++M++LS A+NIF+G E ++  G+FID  ++ R+
Sbjct: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A         +++DP   +G+ ++A QQMVEIA+A+   ++VLI+DEPT++L   E  +L
Sbjct: 141 AAAIFAR-MRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F +++ L+ +GV I++ISH+++E+ +I D+VSV+RDG+YI T  ++  + + I+ MMVGR
Sbjct: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGR 259

Query: 241 KLE-KFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETI 298
            L+ +  I       +VVLEV+ L+ G    +VSF+LR+GEILGFAGL+GAGRTE+   I
Sbjct: 260 ALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAI 319

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
           FG  P   GEI I G +  I  P DA+  GIG + EDRK  GL + M +  N++L S+ R
Sbjct: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379

Query: 359 IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILIL 418
             +  F+  +  +E A   ++   I+    +++   LSGGNQQK+V+AKWL     IL  
Sbjct: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439

Query: 419 DEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDA 478
           DEPTRGIDVGAK+EIY+++  LA++G  ++MISSELPEVL+MS R+ VM  G++ G +  
Sbjct: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499

Query: 479 KEASQEKVMKLAAGLE 494
            +A+QEK+M+LA   E
Sbjct: 500 ADATQEKIMQLATQRE 515


Lambda     K      H
   0.318    0.138    0.385 

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: 628
Number of extensions: 31
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 494
Length of database: 520
Length adjustment: 34
Effective length of query: 460
Effective length of database: 486
Effective search space:   223560
Effective search space used:   223560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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:

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