Alignments for a candidate for gguA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Herbaspirillum seropedicae SmR1

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__HerbieS:HSERO_RS03640
          Length = 502

 Score =  348 bits (892), Expect = e-100
 Identities = 208/504 (41%), Positives = 309/504 (61%), Gaps = 20/504 (3%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +L+MR I K+F    AL +++L ++ GEIHAL+GENGAGKSTLMKVLSGV+     +GEI
Sbjct: 10  LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPD--QGEI 67

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123
             +G     R    S   GI +I+QELA+ P +S+A N+F+G+E+ +  G+I      +R
Sbjct: 68  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 127

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           T  +L+++G       L   + + +QQ VEIA+AL    +++I+DEPTA+L+E ++E L 
Sbjct: 128 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 187

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
           N++   R++G+  I I+H++ EV  +AD++TVLRDG  V  L   ++EI  + I++ MVG
Sbjct: 188 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV--RDEIDSERIVQMMVG 245

Query: 244 RDLEDRYP-----PRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298
           R L + Y      P D     T+++V+              +   +  VR GEV+G AGL
Sbjct: 246 RSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK--------IRPASFDVRAGEVLGFAGL 297

Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358
           +GAGRTE A  +FG     R  GD+L++G+PV +   R A+ AG+AYV EDRK  GL L 
Sbjct: 298 VGAGRTELARLLFGAD--PRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQ 355

Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
             +  N T+   +  ++  ++       VA     RL ++ +        LSGGNQQKV+
Sbjct: 356 MAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVL 415

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           L++WL   P VLILDEPTRG+D+ AK EIY ++++LA+ G  V++ISSE+PE++G CDR+
Sbjct: 416 LARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRV 475

Query: 479 YVMNEGRIVAELPKGEASQESIMR 502
            VM EG I  EL     +QE+IMR
Sbjct: 476 LVMREGMITGELAGAAITQENIMR 499



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 55/226 (24%), Positives = 108/226 (47%), Gaps = 7/226 (3%)

Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAI 339
           L D+++T+R GE+  + G  GAG++     + G     +  G++L+DG+PV +     + 
Sbjct: 26  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ--GEILLDGRPVALRDPGASR 83

Query: 340 DAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRS 399
            AG+  + ++   L +  N ++  N  + +        I  D   M+  +D   R     
Sbjct: 84  AAGINLIYQE---LAVAPNISVAANVFMGSELRTRLGLI--DHAAMRSRTDAVLRQLGAG 138

Query: 400 SGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGK 459
            G       LS   QQ+V +++ L     ++I+DEPT  +      +++ ++ +L  +G 
Sbjct: 139 FGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGL 198

Query: 460 GVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
            ++ IS  M E+    DR+ V+ +G  V EL + E   E I++ ++
Sbjct: 199 AIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 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: 614
Number of extensions: 35
Number of successful extensions: 12
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: 502
Length adjustment: 34
Effective length of query: 478
Effective length of database: 468
Effective search space:   223704
Effective search space used:   223704
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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