Alignments for a candidate for gguA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Cupriavidus basilensis 4G11

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Cup4G11:RR42_RS03360
          Length = 537

 Score =  343 bits (881), Expect = 7e-99
 Identities = 211/508 (41%), Positives = 302/508 (59%), Gaps = 31/508 (6%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +L +RNI KTFPGV+AL  V L    GE+HAL+GENGAGKSTLMK+LSG Y A    GE 
Sbjct: 10  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADP-GGEC 68

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
           H +G          + D+G+ +I+QEL+L P LS+AENI+LG  +   G+++        
Sbjct: 69  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 128

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
              L ++G   SP   +  + + ++QLVEIA+A+    ++L++DEPT  L+  +++ L  
Sbjct: 129 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 188

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           L+ + R +GM  + I+H++ E+ ++AD++TVLRDG  V TLD  +  +S+  +++ MVGR
Sbjct: 189 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD--RAHLSQAALVKMMVGR 246

Query: 245 DLEDRYPPR--DVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302
           DL   Y          E +L V++         D + +   +  +R GEV+G+AGL+GAG
Sbjct: 247 DLSGFYTKTHGQAVEREVMLSVRD-------VADGRRVKGCSFDLRAGEVLGLAGLVGAG 299

Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTV-------RKAIDAGLAYVTEDRKHLGL 355
           RTE A  VFG     R  G+V I         V       R+AIDAG+AY+TEDRK  GL
Sbjct: 300 RTELARLVFGAD--ARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGL 357

Query: 356 VLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGI--FQETVN---LS 410
            L+ ++  N  L     V+    +   +  + A+  RT   I + GI      VN   LS
Sbjct: 358 FLDQSVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALS 413

Query: 411 GGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPE 470
           GGNQQKV+LS+ L   P VLILDEPTRG+D+GAK EIY +IN LA  G  +LMISSE+PE
Sbjct: 414 GGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPE 473

Query: 471 LLGNCDRIYVMNEGRIVAEL-PKGEASQ 497
           ++G CDR+ VM EG +  E+ P G A++
Sbjct: 474 VVGLCDRVLVMREGTLAGEVRPAGSAAE 501



 Score = 71.2 bits (173), Expect = 9e-17
 Identities = 54/231 (23%), Positives = 105/231 (45%), Gaps = 13/231 (5%)

Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337
           + L  + +T   GEV  + G  GAG++   M +   +Y     G+  IDG+ V +   + 
Sbjct: 24  RALRKVELTAYAGEVHALMGENGAGKSTL-MKILSGAYTADPGGECHIDGQRVQIDGPQS 82

Query: 338 AIDAGLAYVTEDRKHL-GLVLNDNILHNTTLANLAGVSKASIIDDIKEM--KVASDFRTR 394
           A D G+A + ++      L + +NI     L     V++  ++        ++ +DF   
Sbjct: 83  ARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADFSPA 142

Query: 395 LRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQL 454
             + S  I Q         +Q V +++ +     +L++DEPT  +       ++ +I QL
Sbjct: 143 ANVASLSIAQ---------RQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 193

Query: 455 AADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
             +G  +L IS  M E+    DR+ V+ +G  V  L +   SQ ++++ ++
Sbjct: 194 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 244


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: 645
Number of extensions: 35
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 537
Length adjustment: 35
Effective length of query: 477
Effective length of database: 502
Effective search space:   239454
Effective search space used:   239454
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