GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Gracilibacillus halophilus YIM-C55.5

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_003463746.1 J416_RS02055 ATP-binding cassette domain-containing protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000359605.1:WP_003463746.1
          Length = 510

 Score =  623 bits (1607), Expect = 0.0
 Identities = 314/510 (61%), Positives = 399/510 (78%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           M++ ILEM +ITKTFPGVKAL++VNLKV+ GEIHALVGENGAGKSTLMKVLSGV+P G+Y
Sbjct: 1   MSDYILEMESITKTFPGVKALDDVNLKVQHGEIHALVGENGAGKSTLMKVLSGVHPYGSY 60

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120
           EG I ++G    FR I  SE+ GI+IIHQELAL P LSIAENIFLGNE  SN ++ WQ T
Sbjct: 61  EGSIVFKGEKSQFRNIKQSENEGIVIIHQELALSPYLSIAENIFLGNERQSNKIMKWQDT 120

Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180
           F+++++LL +VGL+ESPET + +IGVGKQQLVEIAKALSK+VKLLILDEPTA+LNE+DSE
Sbjct: 121 FSQSQQLLDQVGLRESPETSVMNIGVGKQQLVEIAKALSKNVKLLILDEPTAALNETDSE 180

Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240
            LLNLL++ + QG+TSI+I+HKLNEV  +AD IT+LRDG T++TLD   E+ISE+ II+ 
Sbjct: 181 NLLNLLLDLKEQGITSILISHKLNEVSSIADSITILRDGKTIETLDTRTEDISEERIIKG 240

Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           MVGR+L  R+P R   IGET+ EVKNW+ YH Q     ++ D+N+ +RKGE+VG+AGLMG
Sbjct: 241 MVGRELTSRFPERTPNIGETVFEVKNWHVYHPQRSHELLIKDVNMKIRKGEIVGLAGLMG 300

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
           AGRTE  MS+FGKSYG +I+G++  DGK +   TV  AI  G+AYV+EDRK  GL L D+
Sbjct: 301 AGRTELVMSMFGKSYGRKISGELYKDGKQIQAHTVSDAISHGMAYVSEDRKTYGLNLIDD 360

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
           I  N TLANL  +++  ++D  +E++ A      L I++  I Q   NLSGGNQQKVVLS
Sbjct: 361 IKGNITLANLQRIARRKVVDANQEIRDAQHLTETLNIKTPSINQVAGNLSGGNQQKVVLS 420

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           KW+F+ PD+LILDEPTRGIDVGAK+EIY++I+ LA  GK + +ISSE+PE+LG  DRIYV
Sbjct: 421 KWIFTEPDILILDEPTRGIDVGAKFEIYSLIHDLAQQGKCIFVISSELPEVLGLSDRIYV 480

Query: 481 MNEGRIVAELPKGEASQESIMRAIMRSGEK 510
           MNEG I  E  +GEA QE++M  +  +G K
Sbjct: 481 MNEGEITGEFNRGEADQENMMHYMTGAGGK 510


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: 821
Number of extensions: 33
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: 510
Length adjustment: 35
Effective length of query: 477
Effective length of database: 475
Effective search space:   226575
Effective search space used:   226575
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