GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Herbaspirillum seropedicae SmR1

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 HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS03640 HSERO_RS03640 D-ribose
           transporter ATP-binding protein
          Length = 502

 Score =  427 bits (1098), Expect = e-124
 Identities = 219/494 (44%), Positives = 334/494 (67%), Gaps = 7/494 (1%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L+++ I K F    AL  + +   PGE+HA++GENGAGKSTLMK+++GV+ PD+GEI+
Sbjct: 9   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 68

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREA 121
            +GR V    P  +  AGI  ++QEL+V  N+SVA N+FMG E +  +  ID+  M    
Sbjct: 69  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 128

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           +  ++ + G      +  G+ SIA QQ VEIARA+  +++++I+DEPT++L+++ETE+LF
Sbjct: 129 DAVLR-QLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 187

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            VV+ L+++G+AII+ISHR+ E++ + D+V+VLRDG ++G    + +  E+IV+MMVGR 
Sbjct: 188 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 247

Query: 242 LEKFYIKEAHEPGE-----VVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           L +FY  +   P +      V++V+ L+G +    SF +R GE+LGFAGLVGAGRTEL  
Sbjct: 248 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 307

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            +FG  P+ GG+I +EG+ V I+ P  A+  GI  VPEDRK  GL L M++  N ++   
Sbjct: 308 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 367

Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
            R  +   +  +    +A  AI+  +++ A+P+  V  LSGGNQQKV+LA+WL + PK+L
Sbjct: 368 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 427

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           ILDEPTRG+D+ AK+EIY+++ +LA +GV V++ISSELPEV+ + DR+ VM  G + G +
Sbjct: 428 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 487

Query: 477 DAKEASQEKVMKLA 490
                +QE +M+LA
Sbjct: 488 AGAAITQENIMRLA 501



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 59/223 (26%), Positives = 110/223 (49%), Gaps = 5/223 (2%)

Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329
           ++  ++R GEI    G  GAG++ LM+ + G      GEI ++G+ V +  P  +   GI
Sbjct: 28  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 87

Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPD 389
            L+ ++   L +   +S+  NV + S  R + G  I     +   D  ++         D
Sbjct: 88  NLIYQE---LAVAPNISVAANVFMGSELRTRLG-LIDHAAMRSRTDAVLRQLGAGFGASD 143

Query: 390 RKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIM 449
                LS   QQ+V +A+ L  + +I+I+DEPT  +      +++ ++ +L  EG+ +I 
Sbjct: 144 LAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 202

Query: 450 ISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           IS  + EV  ++DR+ V+  G   G +   E   E+++++  G
Sbjct: 203 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 245


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: 678
Number of extensions: 19
Number of successful extensions: 6
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 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