Alignments for a candidate for gguA in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Bradyrhizobium sp. BTAi1

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012044833.1 BBTA_RS22620 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000015165.1:WP_012044833.1
          Length = 499

 Score =  311 bits (797), Expect = 3e-89
 Identities = 184/509 (36%), Positives = 299/509 (58%), Gaps = 26/509 (5%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           ++E++++TK F G+ AL +++  ++ GE+HAL+GENGAGKSTL K+++GVY   +  GE+
Sbjct: 4   VVELKSVTKEFHGIPALRDISFDLRPGEVHALLGENGAGKSTLTKIMAGVYEVTS--GEL 61

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
              G   +F+   ++   GI ++ QE +LVP L++A+NI+LGNE   N +   +  +   
Sbjct: 62  IVNGTKVSFKTPAEALRSGIAMVFQETSLVPSLTVAQNIYLGNERFLNRL---RGIYIAA 118

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           ++ L+ +     P   ++ +G  ++Q+VEIA+A+    +++I DEPTA+L   +      
Sbjct: 119 QQFLQSLNFGVDPTMYVSQLGAAQKQMVEIARAVHHKARVIIFDEPTATLTPEEKHHFFA 178

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           L+   +  G++ I I+H L E   ++D+IT++RDG  V T D   +    D II  MVGR
Sbjct: 179 LVKRLKRDGVSIIFISHALEEALSISDRITIMRDGQHVVTDDA--KNFDRDKIITAMVGR 236

Query: 245 DLEDRYPPR------DVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298
            L D    +        P G  +L V+N +         +++ + + +V  G++ GI GL
Sbjct: 237 TLSDELYGKAGDGHATRPYGRKMLSVQNLSM-------GRMVRNNSFSVYAGQITGIFGL 289

Query: 299 MGAGRTEFAMSVFG---KSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGL 355
           +G+GRTE A  + G   + + H   G+V ++G+ V     R+A+  G+ YVTEDRK  G 
Sbjct: 290 IGSGRTETAKIISGVVKRDFFHG--GEVKLEGRSVRYRVPRQAVRDGIVYVTEDRKIEGF 347

Query: 356 VLNDNILHNTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQ 414
               +I  N  L  LA  ++K+ +I   + M++A+ +  RL +R+       V LSGGNQ
Sbjct: 348 FETKSIAENIYLNLLAADLNKSVVISYAEMMELAATWTKRLNVRAISNAARVVELSGGNQ 407

Query: 415 QKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGN 474
           QKVV+++ L   P ++I DEPTRG+DVGA  E++ +IN+LA  G  V++ISS +PE+L  
Sbjct: 408 QKVVIARALVQQPKLVIFDEPTRGVDVGAIAELHHVINELADAGLAVVVISSYLPEILNL 467

Query: 475 CDRIYVMNEGRIVAELPKGEASQESIMRA 503
            DRI V  +GR+V E    EA++E IM A
Sbjct: 468 ADRILVSRQGRVVEEFSADEATEEKIMYA 496



 Score = 66.2 bits (160), Expect = 3e-15
 Identities = 54/229 (23%), Positives = 109/229 (47%), Gaps = 17/229 (7%)

Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRIT-GDVLIDGKPVDVSTVRKA 338
           L DI+  +R GEV  + G  GAG++     + G    + +T G+++++G  V   T  +A
Sbjct: 20  LRDISFDLRPGEVHALLGENGAGKSTLTKIMAGV---YEVTSGELIVNGTKVSFKTPAEA 76

Query: 339 IDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIR 398
           + +G+A V ++     LV +  +  N  L N         ++ ++ + +A+  +  L+  
Sbjct: 77  LRSGIAMVFQETS---LVPSLTVAQNIYLGN------ERFLNRLRGIYIAA--QQFLQSL 125

Query: 399 SSGI--FQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAA 456
           + G+        L    +Q V +++ +     V+I DEPT  +    K+  + ++ +L  
Sbjct: 126 NFGVDPTMYVSQLGAAQKQMVEIARAVHHKARVIIFDEPTATLTPEEKHHFFALVKRLKR 185

Query: 457 DGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
           DG  ++ IS  + E L   DRI +M +G+ V         ++ I+ A++
Sbjct: 186 DGVSIIFISHALEEALSISDRITIMRDGQHVVTDDAKNFDRDKIITAMV 234


Lambda     K      H
   0.316    0.135    0.374 

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: 555
Number of extensions: 33
Number of successful extensions: 10
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: 512
Length of database: 499
Length adjustment: 34
Effective length of query: 478
Effective length of database: 465
Effective search space:   222270
Effective search space used:   222270
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 (21.6 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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Protein sequences (fasta format)
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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