GapMind for catabolism of small carbon sources

 

Aligments 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_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02712 H281DRAFT_02712
           monosaccharide ABC transporter ATP-binding protein, CUT2
           family
          Length = 505

 Score =  444 bits (1143), Expect = e-129
 Identities = 241/498 (48%), Positives = 343/498 (68%), Gaps = 12/498 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEG-EI 61
           P LE+++I + FPGV AL  V++E   GEV A+ GENGAGKSTLMKI+ G+Y PD G  I
Sbjct: 8   PFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTI 67

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYRE 120
           + EG+ V       A   G+  ++QEL+V+ NL+V ENIF+  E +  +  ID  +MYRE
Sbjct: 68  LVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYRE 127

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A + +     ++IDP  ++ + S+  QQM+EIA+A+  ++K +I+DEPT+SL+  ET  L
Sbjct: 128 AREVLAT-IDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVL 186

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
             +VK L+E+ +A+++ISHRLEEIFE+ D+V+VLRDG  +GT  I ++T+E +V +MV R
Sbjct: 187 LGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVAR 246

Query: 241 KLEKFYIK-EAHEPGEVVLEVKNLSGE-------RFENVSFSLRRGEILGFAGLVGAGRT 292
           +L + Y + ++H   + VLEV+ LS +       R  ++SF+L RGE+LG AGLVG+GRT
Sbjct: 247 ELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGRT 306

Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
           E+ME IFG R   G  + IEGK V I +P DAI  GIG V EDRK  GLIL M++  N S
Sbjct: 307 EIMEMIFGMRACTGS-VKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFS 365

Query: 353 LPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412
           L  L+R     F+   RE+E     ++   I+    ++KV+ LSGGNQQK+V+AKW+A  
Sbjct: 366 LTHLERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVARS 425

Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472
           PK+LI+DEPTRGIDVGAKAE++ ++++LA EG+GVI+ISS+L EVL +SDRI  +  G++
Sbjct: 426 PKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGRI 485

Query: 473 AGIIDAKEASQEKVMKLA 490
           +G +   +ASQEKVM LA
Sbjct: 486 SGELSRAQASQEKVMALA 503



 Score =  100 bits (249), Expect = 1e-25
 Identities = 69/251 (27%), Positives = 127/251 (50%), Gaps = 11/251 (4%)

Query: 250 AHEPGEVVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFG-FRP 303
           +H  G   LE++N+S      +  + V+  +R GE+L  AG  GAG++ LM+ + G + P
Sbjct: 2   SHVTGVPFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAP 61

Query: 304 KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGP 363
             GG I +EG+ V +     A   G+ ++ ++   L ++  +++  N+ L    R + G 
Sbjct: 62  DPGGTILVEGQEVALADSHHARTLGVNIIYQE---LAVVGNLTVGENIFLAREPRTRLG- 117

Query: 364 FISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTR 423
            I   R    A   + T D+    P  +V  LS G QQ + +AK L  + K +I+DEPT 
Sbjct: 118 LIDRPRMYREAREVLATIDM-DIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTA 176

Query: 424 GIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQ 483
            +     + +  I+ +L +  + V+ IS  L E+ +++DR+ V+  G+  G     + ++
Sbjct: 177 SLSHHETSVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTR 236

Query: 484 EKVMKLAAGLE 494
           E +++L    E
Sbjct: 237 ETLVRLMVARE 247


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: 645
Number of extensions: 31
Number of successful extensions: 11
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: 505
Length adjustment: 34
Effective length of query: 460
Effective length of database: 471
Effective search space:   216660
Effective search space used:   216660
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