GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Burkholderia phytofirmans PsJN

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 BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28215 BPHYT_RS28215 D-ribose
           transporter ATP binding protein
          Length = 509

 Score =  425 bits (1092), Expect = e-123
 Identities = 229/492 (46%), Positives = 328/492 (66%), Gaps = 3/492 (0%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P LE++   K F  V AL    +  +PGEVHA++GENGAGKST++KI+AGV+QPD GE++
Sbjct: 9   PRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELV 68

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF-IDYKKMYREA 121
            +G   R+  P+EA +AG+  ++QE ++  +LS+AENIFMG +    I  I Y  M RE 
Sbjct: 69  VDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREV 128

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           +  +    G+++  ++ +   SIA QQ++EIA+A+   A VLI+DEPT++L+  E E+LF
Sbjct: 129 DGLLAS-LGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLF 187

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            +V+ L+E+ VAI+FI+HRL+E+F +  +V+++RDG  +      +L  E IV  MVGR 
Sbjct: 188 TIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRD 247

Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300
           LE FY K    PGEV L V+ L+    F+++SF +R GEI+  AGLVGAGR+E+   IFG
Sbjct: 248 LETFYPKAERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFG 307

Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360
             P   GEI+I GKR+    P  A+  G+ LVPEDR++ GL L +SI  N S+  L R+ 
Sbjct: 308 IDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLGRLV 367

Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
           K   IS + E +LA+       ++   P+  V  LSGGNQQKVVL KWLA  PK+LI+DE
Sbjct: 368 KHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDE 427

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PTRGIDVGAKAE+Y  +++L ++G+ V+MISSELPEVL M+DR+ VM  G+++  I   +
Sbjct: 428 PTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARAD 487

Query: 481 ASQEKVMKLAAG 492
           A +E++M  A G
Sbjct: 488 ADEERIMGAALG 499



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 63/249 (25%), Positives = 116/249 (46%), Gaps = 11/249 (4%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           +P  EV+   +    V   K +S +   GE+ A+ G  GAG+S + + I G+   D GEI
Sbjct: 257 RPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDSGEI 316

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMD---NLSVAENIFMGDEEKRGIFIDYKKMY 118
              G+ +    P+ A+ AG+  V ++         LS+A N  M      G  + +  + 
Sbjct: 317 WIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASM---TVLGRLVKHGLIS 373

Query: 119 REAEKFMKEEFGIEI-----DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLT 173
             +E  +  ++G  +     DP   +G  S   QQ V + + +    KVLI+DEPT  + 
Sbjct: 374 ARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPTRGID 433

Query: 174 QKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKI 233
                +++  +  L   G+A++ IS  L E+  + D+V V+ +G      +  +  +E+I
Sbjct: 434 VGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARADADEERI 493

Query: 234 VEMMVGRKL 242
           +   +G+ +
Sbjct: 494 MGAALGQPM 502


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: 630
Number of extensions: 34
Number of successful extensions: 7
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: 494
Length of database: 509
Length adjustment: 34
Effective length of query: 460
Effective length of database: 475
Effective search space:   218500
Effective search space used:   218500
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 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