GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Cupriavidus basilensis 4G11

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 RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Cup4G11:RR42_RS32900
          Length = 502

 Score =  405 bits (1041), Expect = e-117
 Identities = 217/493 (44%), Positives = 325/493 (65%), Gaps = 10/493 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+ E++ I K FPGV AL  VS   YPGEVH ++GENGAGKS+LMK++ GVY  D GE  
Sbjct: 9   PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFY 68

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI--FIDYKKMYRE 120
           ++G  V    P++ +  GI  +FQE S++  L +A+NIF+G E +  I   +D  +M+ E
Sbjct: 69  HDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAE 128

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A + + +  G+E+     + +  +A QQMVEIA+A+ + A++L+LDEPT++L+ +ETEKL
Sbjct: 129 ARRIL-DILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F V+  LK  GV++I+ISHR+ E+F + D++++LRDG  +G     + T +++V  MVGR
Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGR 247

Query: 241 KLEKFYIKE-AHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETI 298
           K++  Y +E + +PGEV L+V+N+S +    +++  +R GEI+G AGLVG+GR+E+   +
Sbjct: 248 KVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAV 307

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
           FG  P R GEIYI GKR+    P  A E G  L+PE RK  GL LI ++  N+ L  L R
Sbjct: 308 FGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRR 366

Query: 359 IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVL--YLSGGNQQKVVLAKWLALKPKIL 416
                +    + + LA+  I    +R A PD   L  +LSGGNQQK+V+ KWL  + K+ 
Sbjct: 367 AFPARWYRADKAEALAEREIAR--LRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLF 424

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           I DEPTRGIDVGAKAEI+ ++  L K+G GV++ISSELPE++ + DR  VM  G++AG +
Sbjct: 425 IFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEV 484

Query: 477 DAKEASQEKVMKL 489
              E ++E++++L
Sbjct: 485 AHAEMTEERILQL 497



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 64/235 (27%), Positives = 112/235 (47%), Gaps = 9/235 (3%)

Query: 261 KNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEIN 319
           KN  G +  ++VSF++  GE+    G  GAG++ LM+ + G      GE Y +G  V I 
Sbjct: 18  KNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYHDGSPVAIT 77

Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379
            P D +  GI ++ ++     L+  + I  N+ L    R  +G          +   A +
Sbjct: 78  SPADTMGLGIAVIFQE---FSLVPYLDIAQNIFL---GREPRGRIPGSVDAARMHAEARR 131

Query: 380 TFDIRPAYPDRK--VLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIM 437
             DI       +  V  L    QQ V +AK L+   +IL+LDEPT  +      +++ ++
Sbjct: 132 ILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFAVI 191

Query: 438 SQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           ++L  +GV +I IS  + EV  + DRI ++  G+  G     +A+ ++++    G
Sbjct: 192 ARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVG 246


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: 683
Number of extensions: 34
Number of successful extensions: 9
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: 502
Length adjustment: 34
Effective length of query: 460
Effective length of database: 468
Effective search space:   215280
Effective search space used:   215280
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