Alignments for a candidate for gguA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Sinorhizobium meliloti 1021

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Smeli:SM_b20673
          Length = 526

 Score =  373 bits (957), Expect = e-107
 Identities = 221/501 (44%), Positives = 314/501 (62%), Gaps = 8/501 (1%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           IL    I+K+F GV AL++V  +++ GEIHAL+GENGAGKSTLMKVLSGVY    YEG +
Sbjct: 18  ILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYT--DYEGAV 75

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGV-ISWQQTFNR 123
             +G    F  + D+E  GI IIHQEL LVP L +A+NIFLG E    G+ +  + +   
Sbjct: 76  RVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKASLEA 135

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
            R LL ++G++  PE  +  + VG+QQLVEIAKALS   ++LI+DEPT++L+  +   L 
Sbjct: 136 ARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRLF 195

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
            ++ +    G+  I I+H+++EV +++D++TV RDG  V         + E+ II  MVG
Sbjct: 196 KIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARP--MAGLDENTIIAAMVG 253

Query: 244 RDLEDRYP-PRDVPIGETILEVKNWN-AYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301
           R+L D +   R    GE +L V++ + A   +H  R VL  ++  VR GE++GI GL+GA
Sbjct: 254 RNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGA 313

Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361
           GRTE   ++F  + G R  G++ +DG  V++ + R A   G A VTEDRK  GL L+++I
Sbjct: 314 GRTEILETIFASNEGLR-GGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESI 372

Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421
             N  L  +  +++  +     E  +A      L +R +G  Q    LSGGNQQKVV+ K
Sbjct: 373 RDNVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGK 432

Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481
           WL + P VL+LDEPTRGIDVGAK EIY +I +LA DG  ++++SSE+PELL   DRI VM
Sbjct: 433 WLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVM 492

Query: 482 NEGRIVAELPKGEASQESIMR 502
            EGR    + + EAS+E IM+
Sbjct: 493 AEGRQTGLISREEASEERIMQ 513



 Score = 85.1 bits (209), Expect = 6e-21
 Identities = 72/254 (28%), Positives = 114/254 (44%), Gaps = 7/254 (2%)

Query: 252 PRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVF 311
           PRD    E+   +    A  +       L D+   +R GE+  + G  GAG++     + 
Sbjct: 6   PRDSVTTESDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLS 65

Query: 312 GKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLA 371
           G    +   G V +DG+ V  S VR A  AG+A + ++   L LV    +  N  L    
Sbjct: 66  GVYTDYE--GAVRVDGETVRFSNVRDAEAAGIAIIHQE---LNLVPELGVADNIFLGR-E 119

Query: 372 GVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLI 431
            V     +D    ++ A     RL I      +    L  G QQ V ++K L     +LI
Sbjct: 120 RVIAGLFVDRKASLEAARGLLNRLGIELDPEAR-VGQLRVGEQQLVEIAKALSVEARILI 178

Query: 432 LDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELP 491
           +DEPT  +  G    ++ I+ QLAADG G++ IS  + E++   DR+ V  +GR V   P
Sbjct: 179 MDEPTSALSPGECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARP 238

Query: 492 KGEASQESIMRAIM 505
                + +I+ A++
Sbjct: 239 MAGLDENTIIAAMV 252


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: 669
Number of extensions: 34
Number of successful extensions: 11
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: 526
Length adjustment: 35
Effective length of query: 477
Effective length of database: 491
Effective search space:   234207
Effective search space used:   234207
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)
Organisms (tab-delimited)
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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