Alignments for a candidate for mglA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Acidovorax sp. GW101-3H11

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 Ac3H11_1109 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1109
          Length = 513

 Score =  290 bits (742), Expect = 8e-83
 Identities = 174/492 (35%), Positives = 276/492 (56%), Gaps = 14/492 (2%)

Query: 10  IHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVR 69
           I KR+P V A  GVS+   PGE+HA++GENGAGKSTLMKII G  +PDEG + + G+ V+
Sbjct: 3   ITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAVQ 62

Query: 70  WNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEF 129
             +P EA   GI  VFQ  S+ D L+VAEN+++G ++   +    +++  +A      E+
Sbjct: 63  VRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLDKSLTLAEVTQRISAKA-----AEY 117

Query: 130 GIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKE 189
           G++IDP   +   S+   Q VEI RA+    KVLILDEPTS LT +  EKLF V++ L  
Sbjct: 118 GLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLAS 177

Query: 190 KGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKE 249
           +G +I++ISH+L EI  +C   +VLR G+  G  +    T   +  +M+G +        
Sbjct: 178 EGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPPALE-HR 236

Query: 250 AHEPGEVVLEVKNLSGERFE-------NVSFSLRRGEILGFAGLVGAGRTELMETIFGFR 302
           A + G  VL VK LS  R +       ++ F ++ GE++G AG+ G G+ EL+  + G  
Sbjct: 237 AVQTGATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGED 296

Query: 303 PK-RGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361
            +     I + G+      P      G+  VPE+R   G +  M + HN+ L   + +  
Sbjct: 297 QRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAVGG 356

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
             +I     ++ A+  I+ F+++   P      LSGGN QK ++ + +   PK+LI+ +P
Sbjct: 357 SGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVSQP 416

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           T G+DVGA A+I   +  L   G  V+++S EL E+ ++ DR+ V++ G+L+  +   EA
Sbjct: 417 TWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRAEA 476

Query: 482 SQEKVMKLAAGL 493
           + E++ +  +GL
Sbjct: 477 TVERIGEWMSGL 488



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 62/224 (27%), Positives = 113/224 (50%), Gaps = 10/224 (4%)

Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330
           VS ++  GEI    G  GAG++ LM+ I+G      G ++  G+ V++ +P +A   GI 
Sbjct: 16  VSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAVQVRNPQEARALGIA 75

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V +      L   +++  NV L  LD+      ++ +   + A++ +    +RP +   
Sbjct: 76  MVFQH---FSLFDTLTVAENVWL-GLDKSLTLAEVTQRISAKAAEYGLDIDPLRPVHT-- 129

Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450
               LS G  Q+V + + L   PK+LILDEPT  +   A  +++ ++ +LA EG  ++ I
Sbjct: 130 ----LSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLASEGCSILYI 185

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           S +L E+  +     V+  GK+ G+ +  E +   + +L  G E
Sbjct: 186 SHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAE 229


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: 554
Number of extensions: 30
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: 513
Length adjustment: 34
Effective length of query: 460
Effective length of database: 479
Effective search space:   220340
Effective search space used:   220340
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