GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Pseudovibrio axinellae Ad2

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 WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  298 bits (762), Expect = 4e-85
 Identities = 175/501 (34%), Positives = 293/501 (58%), Gaps = 14/501 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L +++I K F  + A   V+++ + GE+ A++GENGAGK+TLM I+ G Y  DEG ++
Sbjct: 9   PLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVM 68

Query: 63  YEGRG-----VRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKM 117
                     +    P  A+ AGI  V Q  ++ +NL+  ENI +G E          K 
Sbjct: 69  VRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA 128

Query: 118 YREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKET 177
             + ++ M+   G+E+D + ++ K ++  +Q VEI +A+Y+ A++L+LDEPT+ LT +E+
Sbjct: 129 RAKLQELMQSS-GLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQES 187

Query: 178 EKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMM 237
           + LF  +K L  KG+AIIFISH++ E+    D+V+VLR G  +         + K+ E+M
Sbjct: 188 DSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAELM 247

Query: 238 VGRKLEKFYIKEAHEPGEVVLEVKNLSG----ERFENVSFSLRRGEILGFAGLVGAGRTE 293
           VG  ++    +E   PGE +L  K +S     E  ENV+ SLR+GEI+G AG+ G G++ 
Sbjct: 248 VGHAVQ-MAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGVSGNGQSM 306

Query: 294 LMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL 353
           L + + G      G + +  + ++ N    AI+ G+  +PEDR   G++  MS+  N+ L
Sbjct: 307 LAKVLSGLEEPTAGAVTLGSQPLKAN-AAAAIQSGVARIPEDRHHDGIVGAMSVEENLVL 365

Query: 354 PSLDR--IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411
             + +   ++   + F   ++ A  AIK +DIR + P      LSGGN QK+VLA+ L  
Sbjct: 366 EEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQ 425

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           +P I++  +P+RG+DVGA A+++R + +    G GV++IS +L E+ Q+SDRIAV+  G 
Sbjct: 426 EPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGH 485

Query: 472 LAGIIDAKEASQEKVMKLAAG 492
           ++  + ++E  +++V  + AG
Sbjct: 486 VSEPMASEELDKKQVGLMMAG 506


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: 642
Number of extensions: 39
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
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 24 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