Alignments for a candidate for gguA in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Azohydromonas australica DSM 1124

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_029001073.1 H537_RS0131585 ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000430725.1:WP_029001073.1
          Length = 510

 Score =  241 bits (616), Expect = 3e-68
 Identities = 159/495 (32%), Positives = 261/495 (52%), Gaps = 11/495 (2%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           LE+  I+K +P VKA + V+L+V  G+IHA++GENGAGKSTLMK++ G       EGEI 
Sbjct: 4   LELVGISKQYPAVKANDGVSLRVAPGQIHAVLGENGAGKSTLMKIIYGAVRPD--EGEIR 61

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125
           + G     R  +++  +GI ++ Q  +L   L+ AEN++LG + +    ++  +   R R
Sbjct: 62  WNGRPVQVRNPHEARALGISMVFQHFSLFDTLTAAENVWLGLDKS----MALPEVVTRMR 117

Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
           E+ K+ GL+  P   +  + VG++Q VEI +AL    +LLILDEPT+ L     E L   
Sbjct: 118 EVSKEYGLEVDPMRPVHSLSVGERQRVEIVRALMGRPQLLILDEPTSVLTPQAVEKLFVT 177

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245
           L +   QG + + I+HKL+E+R +    TVLR G     +D  QE  +   + R M+G +
Sbjct: 178 LRQLAAQGCSILYISHKLDEIRSLCHHCTVLRGGKVTGEVDPGQETNAS--LSRLMIGSE 235

Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305
                     P G+ +L VK      +Q      L DI + VR GE+VG+AG+ G G+ E
Sbjct: 236 PPQLRHAATTP-GDVVLAVKGLRL-ERQDVFGTTLQDIALQVRAGEIVGVAGVSGNGQQE 293

Query: 306 FAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNT 365
              ++ G+       G + +  + +  ++  +    GL +V E+R   G V   ++  N 
Sbjct: 294 LMAALSGEDR-RAARGSITLFDRDIATASPSRRRRLGLHFVPEERLGRGAVPTLSLAENV 352

Query: 366 TLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFS 425
            L     V+    +   +   +A     R  +++ G      +LSGGN QK ++ + + +
Sbjct: 353 LLTRTEPVAAGGWLRRAQVRALAQSLIERFNVKAGGWHSAAKSLSGGNLQKFIVGREIDA 412

Query: 426 NPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGR 485
            P +LI+ +PT G+DVGA  +I   + +L   G  +L++S E+ EL    DR+ V+ +GR
Sbjct: 413 RPKLLIVSQPTWGVDVGAAAQIRGELLKLRDAGCALLVVSEELDELFEISDRLVVIAQGR 472

Query: 486 IVAELPKGEASQESI 500
           +   +P  +A+ E I
Sbjct: 473 LSPSIPTPQATVEQI 487



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 53/225 (23%), Positives = 106/225 (47%), Gaps = 12/225 (5%)

Query: 283 INVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAG 342
           +++ V  G++  + G  GAG++     ++G        G++  +G+PV V    +A   G
Sbjct: 22  VSLRVAPGQIHAVLGENGAGKSTLMKIIYGAVRPDE--GEIRWNGRPVQVRNPHEARALG 79

Query: 343 LAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGI 402
           ++ V +   H  L        N  L     ++   ++  ++E  V+ ++   +       
Sbjct: 80  ISMVFQ---HFSLFDTLTAAENVWLGLDKSMALPEVVTRMRE--VSKEYGLEV-----DP 129

Query: 403 FQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVL 462
            +   +LS G +Q+V + + L   P +LILDEPT  +   A  +++  + QLAA G  +L
Sbjct: 130 MRPVHSLSVGERQRVEIVRALMGRPQLLILDEPTSVLTPQAVEKLFVTLRQLAAQGCSIL 189

Query: 463 MISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRS 507
            IS ++ E+   C    V+  G++  E+  G+ +  S+ R ++ S
Sbjct: 190 YISHKLDEIRSLCHHCTVLRGGKVTGEVDPGQETNASLSRLMIGS 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: 501
Number of extensions: 30
Number of successful extensions: 9
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: 510
Length adjustment: 35
Effective length of query: 477
Effective length of database: 475
Effective search space:   226575
Effective search space used:   226575
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 Apr 09 2024. 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 2024 update 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