GapMind for catabolism of small carbon sources

 

Alignments 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_RS16930 BPHYT_RS16930 arabinose ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__BFirm:BPHYT_RS16930
          Length = 512

 Score =  418 bits (1074), Expect = e-121
 Identities = 224/498 (44%), Positives = 333/498 (66%), Gaps = 13/498 (2%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M   L   +I K FPGV AL GVS +   G+VH ++GENGAGKSTL+KI+ G YQPD G 
Sbjct: 1   MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           ++ +G  VR+   + +I AGI  + QEL  + +L+VAEN+ +G       +++     RE
Sbjct: 61  VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVN----KRE 116

Query: 121 AEKFMKEE---FGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKET 177
           A++F++E     G+ +DP  KL K SIA +QMVEI +A+ + A+V+ LDEPTSSL+ +ET
Sbjct: 117 AKRFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRET 176

Query: 178 EKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGT-DSIENLTKEKIVEM 236
           E LF++V+ L+    A+I+ISHR++EI+E+CD  ++ RDG  I +  ++E +T++ IV  
Sbjct: 177 EVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSE 236

Query: 237 MVGRKLEKFYIKEAHEPGEVVLEVKNLSGERF-ENVSFSLRRGEILGFAGLVGAGRTELM 295
           MVGR++   Y   A   GEV    K + G    +  SF +RRGEI+GF GLVGAGR+ELM
Sbjct: 237 MVGREISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELM 296

Query: 296 ETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS 355
             ++G   K+GGE+ ++GK +++    +AI  GI L PEDRK+ G++ + ++  N+++  
Sbjct: 297 HLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC 356

Query: 356 LDR-IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP- 413
               ++ G F+  K+E E AD  IK   I+     +K+ +LSGGNQQK +L++WLA +P 
Sbjct: 357 RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLA-EPD 415

Query: 414 -KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472
            K++ILDEPTRGIDVGAK EIY ++ QLA+ G  ++MISSELPEVL +SDRI VM  G++
Sbjct: 416 LKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRI 475

Query: 473 AGIIDAKEASQEKVMKLA 490
           +G +  K+A+++ V+ LA
Sbjct: 476 SGELTRKDATEQSVLSLA 493


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: 675
Number of extensions: 37
Number of successful extensions: 11
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: 512
Length adjustment: 34
Effective length of query: 460
Effective length of database: 478
Effective search space:   219880
Effective search space used:   219880
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