Alignments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03878 H281DRAFT_03878 xylose ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Burk376:H281DRAFT_03878
          Length = 519

 Score =  419 bits (1077), Expect = e-121
 Identities = 223/501 (44%), Positives = 330/501 (65%), Gaps = 12/501 (2%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD--EG 59
           +P+L ++ I K F GV AL G+ +   PGE   + GENGAGKSTLMK+++GVY     +G
Sbjct: 3   QPLLTMRGIVKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDG 62

Query: 60  EIIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMY 118
           EI +EG+ ++     +   AGI+ + QEL ++  LSVAENIF+G+E    G  ++Y  MY
Sbjct: 63  EITWEGKPLKATSIRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMY 122

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
           + A++ ++E     I+  + +  Y    QQ++EIA+A+ K+AK+LILDEP+SSLT  E  
Sbjct: 123 QRADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIA 182

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
            L ++V+ LK +GVA ++ISH+L+E+  +CD +SV+RDG ++ T+ +  LT ++I+ +MV
Sbjct: 183 ILLDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMV 242

Query: 239 GRKLEKFYIKEAHEPGEVVLEVKNLS--------GERFENVSFSLRRGEILGFAGLVGAG 290
           GR+++  + +E H  G+V+ E +N++         +R  +VSF LRRGEILG AGLVGAG
Sbjct: 243 GREIKNLFPREPHPIGDVIFEARNVTCFDVTNPRRKRVSDVSFELRRGEILGVAGLVGAG 302

Query: 291 RTELMETIFGFRPKRG-GEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMH 349
           RTELM+ IFG  P      + +EGK V+I  P+DAI  GIG+VPEDRK+ G++  +S+ H
Sbjct: 303 RTELMQAIFGAYPGVSEATVVMEGKTVKIRAPIDAIRAGIGMVPEDRKRHGIVPGLSVGH 362

Query: 350 NVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWL 409
           N++L  L R   G  I    E +     +K   +R A+P   +  LSGGNQQK VL + L
Sbjct: 363 NITLAVLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPMLSIASLSGGNQQKAVLTRML 422

Query: 410 ALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSF 469
              PK+LILDEPTRG+DVGAK EIY+++ QLA+ G+ ++M+SSELPEVL +SDR+ V+  
Sbjct: 423 LTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVLVIGE 482

Query: 470 GKLAGIIDAKEASQEKVMKLA 490
           G+L G       +QE ++  A
Sbjct: 483 GELRGDFVNDGLTQEDILSAA 503



 Score = 88.2 bits (217), Expect = 6e-22
 Identities = 66/222 (29%), Positives = 107/222 (48%), Gaps = 6/222 (2%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQP-DEGEIIYEGRGVRWNHPSEAINAGI 81
           VS E   GE+  + G  GAG++ LM+ I G Y    E  ++ EG+ V+   P +AI AGI
Sbjct: 283 VSFELRRGEILGVAGLVGAGRTELMQAIFGAYPGVSEATVVMEGKTVKIRAPIDAIRAGI 342

Query: 82  VTVFQELS---VMDNLSVAENIFMGDEEK--RGIFIDYKKMYREAEKFMKEEFGIEIDPE 136
             V ++     ++  LSV  NI +   ++   G  ID           MK        P 
Sbjct: 343 GMVPEDRKRHGIVPGLSVGHNITLAVLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPM 402

Query: 137 EKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIF 196
             +   S   QQ   + R +    KVLILDEPT  +      ++++++  L ++G++I+ 
Sbjct: 403 LSIASLSGGNQQKAVLTRMLLTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVM 462

Query: 197 ISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           +S  L E+  I D+V V+ +GE  G    + LT+E I+   +
Sbjct: 463 VSSELPEVLGISDRVLVIGEGELRGDFVNDGLTQEDILSAAI 504



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 65/238 (27%), Positives = 116/238 (48%), Gaps = 7/238 (2%)

Query: 260 VKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKR--GGEIYIEGKRV 316
           VK  SG +  + +  ++  GE +G  G  GAG++ LM+ + G  P     GEI  EGK +
Sbjct: 12  VKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDGEITWEGKPL 71

Query: 317 EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADW 376
           +     D    GI ++ ++   L L+  +S+  N+ L +   +  G  +++    + AD 
Sbjct: 72  KATSIRDTERAGIIIIHQE---LMLVPELSVAENIFLGNEITLPGGR-MNYAAMYQRADE 127

Query: 377 AIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRI 436
            ++   I      + V+   GG+QQ + +AK L  + K+LILDEP+  +     A +  I
Sbjct: 128 LLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAILLDI 187

Query: 437 MSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           +  L + GV  + IS +L EV  + D I+V+  G+          + ++++ L  G E
Sbjct: 188 VRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGRE 245


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: 686
Number of extensions: 28
Number of successful extensions: 9
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: 494
Length of database: 519
Length adjustment: 34
Effective length of query: 460
Effective length of database: 485
Effective search space:   223100
Effective search space used:   223100
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources