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

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG 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_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Burk376:H281DRAFT_00426
          Length = 503

 Score =  434 bits (1116), Expect = e-126
 Identities = 230/495 (46%), Positives = 330/495 (66%), Gaps = 6/495 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M P++ VK + K FPGV AL  V  +   GEVHA++GENGAGKSTLMKI+AGVY  D GE
Sbjct: 1   MTPLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGE 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKR--GIFIDYKKMY 118
           I+  G+ V    P +A  AGI  + QEL +M++L+VA+NIF+G E +   G+F+D  K+ 
Sbjct: 61  ILLGGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLN 120

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
            +A + +     + IDP   +G  ++A QQMVEIA+A+   ++VLI+DEPTS+L   E  
Sbjct: 121 AKAREILSR-MHVNIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIA 179

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           +LF +++ LK++GV +++ISH+++E+ +I D+V+VLRDGEY+ T +  + + E I+ MMV
Sbjct: 180 ELFRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMV 239

Query: 239 GRKLEKFY-IKEAHEPGEVVLEVKNL-SGERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           GR L        A   GE+ LEV+NL +G    +VSF+LR+GEILGFAGL+GAGRTE+  
Sbjct: 240 GRTLSDVAPAGRAASQGEIALEVRNLHAGPLVRDVSFTLRKGEILGFAGLMGAGRTEVAR 299

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            +FG  P   GEI+++G +  I  P DA+  GIG + EDRK+ GL   M +  N+ + +L
Sbjct: 300 AVFGADPVESGEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSNL 359

Query: 357 DR-IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415
              +    F+   R +  A   I    IR     ++V  LSGGNQQK+V+AKWL     +
Sbjct: 360 RNFLSLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLERDCDV 419

Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475
           L  DEPTRGIDVGAK+EIY+++  LA EG  ++MISSELPE+L+MSDR+ VM  G++ G 
Sbjct: 420 LFFDEPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITGE 479

Query: 476 IDAKEASQEKVMKLA 490
           + A++A+QE++M LA
Sbjct: 480 LPAEQATQERIMHLA 494



 Score =  108 bits (270), Expect = 4e-28
 Identities = 70/233 (30%), Positives = 124/233 (53%), Gaps = 5/233 (2%)

Query: 261 KNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEIN 319
           K+  G R   +V F L  GE+    G  GAG++ LM+ + G   +  GEI + G+ VE+ 
Sbjct: 12  KSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEILLGGQPVELQ 71

Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379
            P DA   GIG++ ++   L L+  +++  N+ +    R + G F+   +    A   + 
Sbjct: 72  SPRDAQAAGIGIIHQE---LQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLNAKAREILS 128

Query: 380 TFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQ 439
              +    P   V  L+  +QQ V +AK L+   ++LI+DEPT  ++    AE++RI+ +
Sbjct: 129 RMHVN-IDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFRIIRE 187

Query: 440 LAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           L + GVGV+ IS ++ E+ Q++DR+ V+  G+    + A + S E ++ +  G
Sbjct: 188 LKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVG 240



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 63/246 (25%), Positives = 114/246 (46%), Gaps = 10/246 (4%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           LEV+++H        ++ VS     GE+    G  GAG++ + + + G    + GEI  +
Sbjct: 260 LEVRNLHAG----PLVRDVSFTLRKGEILGFAGLMGAGRTEVARAVFGADPVESGEIFVK 315

Query: 65  GRGVRWNHPSEAINAGIVTVFQE---LSVMDNLSVAENIFMGDEEK---RGIFIDYKKMY 118
           G       PS+A+  GI  + ++     +   + V  NI M +         F+   +M 
Sbjct: 316 GAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSNLRNFLSLNFFLRRARMR 375

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
           R A  F+           +++   S   QQ + IA+ + +   VL  DEPT  +      
Sbjct: 376 RRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKS 435

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           +++++++SL ++G AI+ IS  L EI  + D+V V+ +G   G    E  T+E+I+ +  
Sbjct: 436 EIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITGELPAEQATQERIMHLAT 495

Query: 239 GRKLEK 244
            R+  K
Sbjct: 496 QRQTLK 501


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: 632
Number of extensions: 35
Number of successful extensions: 8
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: 503
Length adjustment: 34
Effective length of query: 460
Effective length of database: 469
Effective search space:   215740
Effective search space used:   215740
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