Aligments for a candidate for gguA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for gguA in Dinoroseobacter shibae DFL-12

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  263 bits (672), Expect = 1e-74
 Identities = 177/507 (34%), Positives = 279/507 (55%), Gaps = 27/507 (5%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           +E+R I+K F  V+A ++++++V  G IH ++GENGAGKSTLM +L G Y A    GEI 
Sbjct: 26  IELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADA--GEIF 83

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125
            +G          +   GI ++ Q   LV   ++ EN+ LG E  +    S  +     R
Sbjct: 84  IKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEEGALLRPSLAKARKLLR 143

Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
           EL ++  L  +P+ LI D+ VG QQ VEI KAL +   +LILDEPT  L  ++++ L  +
Sbjct: 144 ELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRI 203

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDG---MTVKTLDCHQEEISEDVIIRNMV 242
           L   + +G T I+ITHKL E+ +  D ++V+R G    TVKT D   E+++E      MV
Sbjct: 204 LEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAE-----LMV 258

Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302
           GR +  R        G  IL V +      Q  +R  +  I++ VR GEV+GIAG+ G G
Sbjct: 259 GRKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVER--VKGISLQVRAGEVLGIAGVAGNG 316

Query: 303 RTEFAMSVFGKSYGHR-ITGDVLIDGKPVDVS------TVRKAIDAGLAYVTEDRKHLGL 355
           ++E  + V G   G R  TG V + G+ +D++        R+A   G+A+V EDR+  GL
Sbjct: 317 QSEL-LEVLG---GMRPATGRVTVSGQQIDLTGKHSNGKTRRA--QGIAHVPEDRQAEGL 370

Query: 356 VLNDNILHNTTLA--NLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGN 413
           +++ +   N      +    ++  ++D+      A     R  +R +  +    N SGGN
Sbjct: 371 IMDYHAWENVAFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGN 430

Query: 414 QQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLG 473
           QQK+VL++ +  NP++L++ +PTRG+D+GA   I+  I  L   GK +L++S E+ E+L 
Sbjct: 431 QQKIVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILS 490

Query: 474 NCDRIYVMNEGRIVAELPKGEASQESI 500
             DR+ VM +GRI+ E P  E +++ +
Sbjct: 491 LSDRVAVMFDGRIMGERPAAETNEKEL 517


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: 662
Number of extensions: 42
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 548
Length adjustment: 35
Effective length of query: 477
Effective length of database: 513
Effective search space:   244701
Effective search space used:   244701
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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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, or view the source code.

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