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_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS27185 BPHYT_RS27185 D-ribose
           transporter ATP-binding protein
          Length = 516

 Score =  433 bits (1113), Expect = e-126
 Identities = 231/493 (46%), Positives = 329/493 (66%), Gaps = 3/493 (0%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           + IL++K + KRFPGV AL G+ ++   GEVHA+ GENGAGKSTLMKII+G Y+ DEG +
Sbjct: 21  REILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVV 80

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREA 121
            Y G  V+++  S+A  AGI  + QEL+++ +LSVAENI++  E KRG F+DY+ +   A
Sbjct: 81  RYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSNA 140

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           ++ + +  G+ + P   +G  S+A QQMVEIA+A+   A+VLI+DEPTSSLT+ ET +LF
Sbjct: 141 QRCL-QRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLF 199

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            +++ L+  GVAI++ISHRL+E+ EI D+V+VLRDG +I T    + T  +IV  MVGR 
Sbjct: 200 RIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRP 259

Query: 242 LEKFYIKEAHEPG-EVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
           L+  Y      P  +++L V++L     F  +SF LR+GEILGFAGL+GAGRTE    IF
Sbjct: 260 LDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIF 319

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359
           G      G I +  + V I  P +AI  GI  + EDRKK GL L M +  N++L ++  I
Sbjct: 320 GAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAI 379

Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
               F+ F  E  +A+  ++   IR     +    LSGGNQQK+V++KWL    +IL  D
Sbjct: 380 SSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFD 439

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
           EPTRGIDVGAK  IY +M +LA +GVGV++ISSELPE+L M+DRIAV   G++  +++ +
Sbjct: 440 EPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETR 499

Query: 480 EASQEKVMKLAAG 492
           + SQE+++  A+G
Sbjct: 500 QTSQEEILHHASG 512



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 56/225 (24%), Positives = 107/225 (47%), Gaps = 9/225 (4%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82
           +S E   GE+    G  GAG++   + I G  +PD G I      V    P EAI  GI 
Sbjct: 291 LSFELRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIA 350

Query: 83  TVFQELS---VMDNLSVAENIFMGDEE---KRGIFIDYKKMYREAEKFMKEEFGIEIDPE 136
            + ++     +  ++ V+ NI + +      RG F+ + +    AE++++E  GI     
Sbjct: 351 YLSEDRKKDGLALSMPVSANITLANVRAISSRG-FLRFSEETAIAERYVRE-LGIRTPTV 408

Query: 137 EKLGK-YSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAII 195
           +++ +  S   QQ + I++ +Y+ +++L  DEPT  +       ++ ++  L   GV ++
Sbjct: 409 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVV 468

Query: 196 FISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
            IS  L E+  + D+++V  +G           ++E+I+    GR
Sbjct: 469 LISSELPELLGMTDRIAVFHEGRITAVLETRQTSQEEILHHASGR 513


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: 617
Number of extensions: 28
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: 516
Length adjustment: 34
Effective length of query: 460
Effective length of database: 482
Effective search space:   221720
Effective search space used:   221720
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