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

GapMind for catabolism of small carbon sources

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

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  298 bits (763), Expect = 3e-85
 Identities = 190/499 (38%), Positives = 287/499 (57%), Gaps = 14/499 (2%)

Query: 2   ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61
           A  +L++  I K F G+  L +V L +  GEIHAL+G+NGAGKSTL+KVL+GV  A    
Sbjct: 15  AAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASG-- 72

Query: 62  GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNE----VASNGVISW 117
           G++   G      +   ++ +GI  ++QE+ L P LS+AENIF G      +A    I W
Sbjct: 73  GQMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDW 132

Query: 118 QQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNES 177
                R R+L+ ++GL+     L++D  V  QQLV IA+ALS   ++LILDEPT+SL++ 
Sbjct: 133 ATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDD 192

Query: 178 DSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVI 237
           + + L  +L   R++G++ + +TH LN+V  V+D+ITVLR+G  V   +   +++    +
Sbjct: 193 EVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVG--EWLAKDLGPQAL 250

Query: 238 IRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQV-LHDINVTVRKGEVVGIA 296
           I  M+GRDL       + P     ++ ++ N    +   +   L  +++ +R GEVVG+A
Sbjct: 251 IAAMLGRDLA---AASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLA 307

Query: 297 GLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLV 356
           GL+G+GRTE A  +FG     R  G + IDG+ V  +    AI  GLA   E+RK  G+V
Sbjct: 308 GLLGSGRTELARLLFGLEQPDR--GALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIV 365

Query: 357 LNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQK 416
              ++  N  LA  A +     +   ++ ++A  +   L I++  + +    LSGGNQQK
Sbjct: 366 AELSVRENIALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQK 425

Query: 417 VVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCD 476
            +L++W+   P +LILDEPTRGIDV AK EI   I +LA  G  VL ISSEM E++    
Sbjct: 426 AILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAH 485

Query: 477 RIYVMNEGRIVAELPKGEA 495
           RI V+ + R V ELP G +
Sbjct: 486 RIVVLRDRRKVGELPAGSS 504



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 63/220 (28%), Positives = 113/220 (51%), Gaps = 14/220 (6%)

Query: 21  LENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIHYEGAVRNFRAINDSE 80
           L+ ++L+++ GE+  L G  G+G++ L ++L G+       G +  +G V  F    D+ 
Sbjct: 291 LQPLDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPD--RGALRIDGQVVKFANPMDAI 348

Query: 81  DIGIIIIHQEL---ALVPLLSIAENIFLGNEVASNGV---ISWQQTFNRTRELLKKVGLK 134
             G+ +  +E     +V  LS+ ENI L  + A  GV   +S  +        +K +G+K
Sbjct: 349 RHGLALCPEERKTDGIVAELSVRENIALALQ-ARMGVGKFLSRSEQTELAERYVKLLGIK 407

Query: 135 ESPETLITDIGV---GKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNLLMEFRN 191
              ET+   IG+   G QQ   +A+ ++   +LLILDEPT  ++ +  + +++ ++    
Sbjct: 408 T--ETVDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQ 465

Query: 192 QGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEE 231
            GM  + I+ +++EV +VA +I VLRD   V  L     E
Sbjct: 466 AGMAVLFISSEMSEVVRVAHRIVVLRDRRKVGELPAGSSE 505



 Score = 54.3 bits (129), Expect = 1e-11
 Identities = 50/237 (21%), Positives = 107/237 (45%), Gaps = 8/237 (3%)

Query: 271 HQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPV 330
           H+Q     VL D+ + +  GE+  + G  GAG++     + G        G + + G+ V
Sbjct: 25  HKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASG--GQMRLGGQAV 82

Query: 331 DVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANL--AGVSKASIIDDIKEMKVA 388
              +   A   G++ V ++   + L  N ++  N         G+++   ID     + A
Sbjct: 83  WPDSPLAAQRLGISTVYQE---VNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQRA 139

Query: 389 SDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIY 448
            D   R+ ++   + +   +     QQ V +++ L     VLILDEPT  +D     +++
Sbjct: 140 RDLVARIGLQID-VTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQKLF 198

Query: 449 TIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
            ++ +L ++G  ++ ++  + ++    DRI V+  G  V E    +   ++++ A++
Sbjct: 199 EVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255


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: 578
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 512
Length of database: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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