GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Azospirillum brasilense Sp245

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  709 bits (1831), Expect = 0.0
 Identities = 358/509 (70%), Positives = 424/509 (83%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           +A  ILEM+ ITKTFPGVKAL++VNL V+EGEIHAL+GENGAGKSTLMKVLSGVYP G++
Sbjct: 1   LAMPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSF 60

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120
           +GEI + G  + FR I DSE +GIIIIHQELALVPLLSI EN+FLGNE AS GVI W   
Sbjct: 61  DGEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAA 120

Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180
             R RELL+ VGL + PETLITDIGVGKQQLVEIAKALSK VKLLILDEPTASLNESDS+
Sbjct: 121 TLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSD 180

Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240
           ALL LL++F+ +G+ SI+I+HKLNE+ KVAD++T+LRDG TV+TLDC +  +S+D IIR 
Sbjct: 181 ALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRG 240

Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           MVGR L DRYP R    G+ + EVK W+A H  H  R+V+ D+N+TVR+GEVVGIAGLMG
Sbjct: 241 MVGRALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMG 300

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
           AGRTEFAMS+FG+SYG  I G   +DG+ +DVST+ +A+  GLAY TEDRKHLGLVL+++
Sbjct: 301 AGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDND 360

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
           I HN TLANL GV+K  +ID  +E++VA +FR RLRIR + +FQETVNLSGGNQQKVVLS
Sbjct: 361 IRHNVTLANLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLS 420

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           KWLF++P VLILDEPTRGIDVGAKYEIYTIINQL A+G+GV++ISSEMPELLG  DRIYV
Sbjct: 421 KWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYV 480

Query: 481 MNEGRIVAELPKGEASQESIMRAIMRSGE 509
           MN G +VAE+P  EASQE IM AIMRSGE
Sbjct: 481 MNAGEMVAEMPAAEASQEKIMGAIMRSGE 509


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: 846
Number of extensions: 28
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: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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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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