Alignments for a candidate for gguA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Paraburkholderia bryophila 376MFSha3.1

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_03878 H281DRAFT_03878 xylose ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Burk376:H281DRAFT_03878
          Length = 519

 Score =  413 bits (1061), Expect = e-120
 Identities = 230/508 (45%), Positives = 325/508 (63%), Gaps = 5/508 (0%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           M   +L MR I K F GVKAL+ ++L V  GE   L GENGAGKSTLMKVLSGVYP GT+
Sbjct: 1   MTQPLLTMRGIVKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTW 60

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVA-SNGVISWQQ 119
           +GEI +EG      +I D+E  GIIIIHQEL LVP LS+AENIFLGNE+    G +++  
Sbjct: 61  DGEITWEGKPLKATSIRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAA 120

Query: 120 TFNRTRELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178
            + R  ELL+++G+   +    + + G G QQL+EIAKAL+K  KLLILDEP++SL  S+
Sbjct: 121 MYQRADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSE 180

Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238
              LL+++ + + +G+  + I+HKL+EV  V D I+V+RDG  V T   H   ++ D II
Sbjct: 181 IAILLDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHA--LTTDRII 238

Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298
             MVGR++++ +P    PIG+ I E +N   +   +  R+ + D++  +R+GE++G+AGL
Sbjct: 239 SLMVGREIKNLFPREPHPIGDVIFEARNVTCFDVTNPRRKRVSDVSFELRRGEILGVAGL 298

Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358
           +GAGRTE   ++FG +Y       V+++GK V +     AI AG+  V EDRK  G+V  
Sbjct: 299 VGAGRTELMQAIFG-AYPGVSEATVVMEGKTVKIRAPIDAIRAGIGMVPEDRKRHGIVPG 357

Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
            ++ HN TLA L   S    ID   E+        RL +R++       +LSGGNQQK V
Sbjct: 358 LSVGHNITLAVLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPMLSIASLSGGNQQKAV 417

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           L++ L ++P VLILDEPTRG+DVGAK+EIY +I QLA  G  ++M+SSE+PE+LG  DR+
Sbjct: 418 LTRMLLTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRV 477

Query: 479 YVMNEGRIVAELPKGEASQESIMRAIMR 506
            V+ EG +  +      +QE I+ A +R
Sbjct: 478 LVIGEGELRGDFVNDGLTQEDILSAAIR 505



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 64/235 (27%), Positives = 109/235 (46%), Gaps = 6/235 (2%)

Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRI-TGDVLIDGKPVDVSTVR 336
           + L  I++TV  GE VG+ G  GAG++   M V    Y H    G++  +GKP+  +++R
Sbjct: 19  KALDGIDLTVSPGECVGLCGENGAGKSTL-MKVLSGVYPHGTWDGEITWEGKPLKATSIR 77

Query: 337 KAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLR 396
               AG+  + ++   L LV   ++  N  L N   +    + +     + A +    L 
Sbjct: 78  DTERAGIIIIHQE---LMLVPELSVAENIFLGNEITLPGGRM-NYAAMYQRADELLRELG 133

Query: 397 IRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAA 456
           I      Q  +N  GG+QQ + ++K L     +LILDEP+  +       +  I+  L  
Sbjct: 134 ISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAILLDIVRDLKR 193

Query: 457 DGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGEKN 511
            G   + IS ++ E+   CD I V+ +GR VA  P    + + I+  ++    KN
Sbjct: 194 RGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGREIKN 248


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: 671
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: 519
Length adjustment: 35
Effective length of query: 477
Effective length of database: 484
Effective search space:   230868
Effective search space used:   230868
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 17 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