GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA 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)



>FitnessBrowser__HerbieS:HSERO_RS03640
          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:

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