GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Oscillibacter ruminantium GH1

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_040659172.1 ON16_RS02720 ATP-binding cassette domain-containing protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000307265.1:WP_040659172.1
          Length = 516

 Score =  612 bits (1579), Expect = e-180
 Identities = 308/507 (60%), Positives = 400/507 (78%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           MA+ +LEMR+I K FPGV+AL+NVNL+V++GEIHALVGENGAGKSTLM VLSG+YP GTY
Sbjct: 1   MASKLLEMRSIIKEFPGVRALDNVNLEVEQGEIHALVGENGAGKSTLMNVLSGIYPYGTY 60

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120
           +G+I Y+G V  F  INDSE  G++IIHQELALVP L+I EN+FLGNE      I W +T
Sbjct: 61  QGDIVYDGEVCKFGKINDSESKGVVIIHQELALVPYLTIGENMFLGNEQGRASRIDWDKT 120

Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180
           ++   + LK VGL+ESP TLI DIGVGKQQLVEIAKAL+K+V+LLILDEPTASLNE+DS+
Sbjct: 121 YDLAAKYLKTVGLEESPRTLIKDIGVGKQQLVEIAKALTKNVRLLILDEPTASLNETDSQ 180

Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240
            LL+LL++F+ QGMT III+HKL+EV  VAD+IT++RDG T++TL    ++  E+ II+ 
Sbjct: 181 KLLDLLLQFKAQGMTCIIISHKLSEVSYVADKITIIRDGATIETLVKGVDDFHEERIIKG 240

Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           MVGR+L DR+P R+  IG+ ++EV++W A H  +  R V + +++ VR+GE+VG++GLMG
Sbjct: 241 MVGRELVDRFPKRESHIGDVVMEVQDWCAEHPTYAGRMVCNHVSMNVRRGEIVGVSGLMG 300

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
           AGRTE AMS+FG+SYG  I G +L++G+ V + +V  AI+  LAYVTEDRK  GL+L++ 
Sbjct: 301 AGRTELAMSIFGRSYGANIKGSLLLNGQEVRLHSVTDAINHKLAYVTEDRKGNGLILSET 360

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
           I  NTT+A +  +S+  ++D   E+K A++++  LR + +GI Q   NLSGGNQQKV+LS
Sbjct: 361 IRENTTMARMERISRHQVLDKDLEIKYANEYKEILRTKCAGIEQNVGNLSGGNQQKVLLS 420

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           KW+F+ PDVLILDEPTRGIDVGAKYEIY I+N L + GK VLMISSEMPELLG CDRIYV
Sbjct: 421 KWMFAEPDVLILDEPTRGIDVGAKYEIYCIMNDLVSQGKAVLMISSEMPELLGMCDRIYV 480

Query: 481 MNEGRIVAELPKGEASQESIMRAIMRS 507
           MNEG +V EL   +ASQESIM  I++S
Sbjct: 481 MNEGSVVGELTHEQASQESIMACILKS 507


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: 762
Number of extensions: 22
Number of successful extensions: 5
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: 516
Length adjustment: 35
Effective length of query: 477
Effective length of database: 481
Effective search space:   229437
Effective search space used:   229437
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 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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