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_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  436 bits (1122), Expect = e-127
 Identities = 234/493 (47%), Positives = 330/493 (66%), Gaps = 3/493 (0%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           + IL++K + KRFPGV AL G+ ++   GEVHA+ GENGAGKSTLMKII+G Y  D+G I
Sbjct: 20  REILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVI 79

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREA 121
            YEG+ V++   S+A  AGI  + QEL+++ +LSVAENI++  E KRG F+DY+ +   A
Sbjct: 80  CYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNANA 139

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           ++ + +  G+ + P   +G  SIA QQMVEIA+A+   A+VLI+DEPTSSLT+ ET +LF
Sbjct: 140 QRCL-QRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLF 198

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            +++ L+  GVAI++ISHRL+E+ EI D+V+VLRDG +I T    + T  +IV  MVGR 
Sbjct: 199 RIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRA 258

Query: 242 LEKFYIKEAHEPGE-VVLEVKNLSG-ERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
           L+  Y      P E V++ V++L   + F  +SF LR+GEILGFAGL+GAGRTE+   IF
Sbjct: 259 LDDAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIF 318

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359
           G      G I +    V I  P +AI  GI  + EDRKK GL L M +  N++L ++  I
Sbjct: 319 GAERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAI 378

Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
               F+ F  E  +A+  ++   IR     +    LSGGNQQK+V++KWL    +IL  D
Sbjct: 379 SSRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFD 438

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
           EPTRGIDVGAK  IY++M +LA +GVGV++ISSELPE+L M+DRIAV   G +  +++ +
Sbjct: 439 EPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETR 498

Query: 480 EASQEKVMKLAAG 492
           + SQE+++  A+G
Sbjct: 499 QTSQEEILHYASG 511



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 54/225 (24%), Positives = 107/225 (47%), Gaps = 9/225 (4%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82
           +S +   GE+    G  GAG++ + + I G  + D G I      V    P EAI  GI 
Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349

Query: 83  TVFQELS---VMDNLSVAENIFMGDEE---KRGIFIDYKKMYREAEKFMKEEFGIEIDPE 136
            + ++     +  ++ VA NI + +      RG F+ + +    AE++++E   I     
Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSNVRAISSRG-FLRFSEETAIAERYVRE-LAIRTPTV 407

Query: 137 EKLGK-YSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAII 195
           +++ +  S   QQ + I++ +Y+ +++L  DEPT  +       +++++  L   GV ++
Sbjct: 408 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVV 467

Query: 196 FISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
            IS  L E+  + D+++V  +G           ++E+I+    GR
Sbjct: 468 LISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASGR 512


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: 627
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: 515
Length adjustment: 34
Effective length of query: 460
Effective length of database: 481
Effective search space:   221260
Effective search space used:   221260
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