Alignments for a candidate for gguA in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Beijerinckia indica ATCC 9039

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012385783.1 BIND_RS14440 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000019845.1:WP_012385783.1
          Length = 518

 Score =  357 bits (917), Expect = e-103
 Identities = 210/508 (41%), Positives = 317/508 (62%), Gaps = 25/508 (4%)

Query: 4   TILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVY---PAGTY 60
           TILEMRN++KTF  VKAL +V+L+++EGEIHAL+GENGAGKSTLMK+LSG Y   P  T 
Sbjct: 10  TILEMRNVSKTFGSVKALRDVSLEIREGEIHALMGENGAGKSTLMKILSGAYIPDPGST- 68

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120
              I  +    +      + ++GI II+QELAL P L++AENI+LG E+   G++     
Sbjct: 69  ---ILLDNKPVSITGPLAARELGISIIYQELALAPNLTVAENIYLGREIRRGGLVDRAAM 125

Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180
              + ++L+++G     + L+  + + ++QLVEIA+A+    ++L++DEPT +L E +++
Sbjct: 126 IAGSAKVLQRLGATFQAKDLVQSLSIAERQLVEIARAVHAHSRILVMDEPTTTLTERETD 185

Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240
            L   +   R  G++ I I+H++NE+  ++D++++LRDG  + TLD   +EI+ D +++ 
Sbjct: 186 RLFETVRALREDGLSIIYISHRMNEIYALSDRVSILRDGTYIGTLD--HDEITPDAVVKM 243

Query: 241 MVGRDLEDRYPPRDVP---IGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAG 297
           MVGRDL   Y          G  IL VKN         D + + D +  + +GEV+GIAG
Sbjct: 244 MVGRDLTSFYKKEHDAHDGRGNIILSVKNIG-------DSKRIFDCSFDLHEGEVLGIAG 296

Query: 298 LMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVL 357
           L+G+GRTE A  ++G     R +G ++++G+   +++V +AI+AGL Y+TEDRK LGL L
Sbjct: 297 LVGSGRTELARLIYG--VDRRRSGIIMLNGESKKIASVSEAIEAGLLYLTEDRKQLGLFL 354

Query: 358 NDNILHNTTLANLA-GVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQK 416
           + ++  N  L   +    K   +   K  + A      L I+          LSGGNQQK
Sbjct: 355 DMSVGENINLGVASRDAYKGCFLKLGKARERADAAIGDLSIKVKSPKTPVGALSGGNQQK 414

Query: 417 VVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCD 476
           V+LS+ L   P VLILDEPTRGID+GAK EIY +IN L   G GV++ISSE+PE++G CD
Sbjct: 415 VLLSRLLELKPRVLILDEPTRGIDIGAKSEIYRLINDLVKSGIGVIVISSELPEIVGVCD 474

Query: 477 RIYVMNEGRIVAELPKGEA---SQESIM 501
           R+ VM+EGRI   +   +A   +QE+I+
Sbjct: 475 RVLVMSEGRIAGTVGGPDAPPITQENII 502



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 53/247 (21%), Positives = 123/247 (49%), Gaps = 12/247 (4%)

Query: 260 TILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRI 319
           TILE++N +   +     + L D+++ +R+GE+  + G  GAG++   M +   +Y    
Sbjct: 10  TILEMRNVS---KTFGSVKALRDVSLEIREGEIHALMGENGAGKSTL-MKILSGAYIPDP 65

Query: 320 TGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASII 379
              +L+D KPV ++    A + G++ + ++   L L  N  +  N  L     + +  ++
Sbjct: 66  GSTILLDNKPVSITGPLAARELGISIIYQE---LALAPNLTVAENIYLGR--EIRRGGLV 120

Query: 380 DDIKEMKVASDFRTRLRIRSSGIFQETV-NLSGGNQQKVVLSKWLFSNPDVLILDEPTRG 438
           D  +   +A   +   R+ ++   ++ V +LS   +Q V +++ + ++  +L++DEPT  
Sbjct: 121 D--RAAMIAGSAKVLQRLGATFQAKDLVQSLSIAERQLVEIARAVHAHSRILVMDEPTTT 178

Query: 439 IDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQE 498
           +       ++  +  L  DG  ++ IS  M E+    DR+ ++ +G  +  L   E + +
Sbjct: 179 LTERETDRLFETVRALREDGLSIIYISHRMNEIYALSDRVSILRDGTYIGTLDHDEITPD 238

Query: 499 SIMRAIM 505
           ++++ ++
Sbjct: 239 AVVKMMV 245


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: 644
Number of extensions: 41
Number of successful extensions: 11
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: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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