GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pbgal in Azospirillum brasilense Sp245

Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate AZOBR_RS26030 AZOBR_RS26030 beta-glucosidase

Query= CAZy::BAD76141.1
         (470 letters)



>FitnessBrowser__azobra:AZOBR_RS26030
          Length = 444

 Score =  283 bits (723), Expect = 1e-80
 Identities = 167/461 (36%), Positives = 246/461 (53%), Gaps = 24/461 (5%)

Query: 11  YRFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYK 70
           + FP  F WG++T+A QIEGA +E G+G  +WD +   E  R   G    VA D YHR+ 
Sbjct: 4   FTFPKDFLWGASTAAYQIEGAIHEDGRGPCVWDTF--TEAGRIQDGSSAAVACDHYHRWA 61

Query: 71  EDIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYHF 130
           ED ALMK+ G N++RFSI+W R++P G G VN   + FY+ ++D LLA+GI P   LYH+
Sbjct: 62  EDTALMKDAGFNAYRFSIAWPRILPSGTGAVNAAGLDFYDRLVDGLLADGIRPMACLYHW 121

Query: 131 DMPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYP 190
           D+P  ++  GGW+ REVV  +A YA +      DRVK W   NEP V    GY    H P
Sbjct: 122 DLPQPLEDRGGWQGREVVGPFADYARIVAARLADRVKDWMMLNEPNVVATHGYGTGEHAP 181

Query: 191 -NVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAH 249
            + +     ++  +H  +A   A+ A   A      +G ++NL P    S  P DV AA 
Sbjct: 182 GHKLGETGILRALHHQNLAQGAALRAL-SAEHSGLTLGTVINLQPCRAESDRPQDVAAAA 240

Query: 250 IADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPR 309
             D ++NR  LD  ++G+ P+ + E + ++  LP     D E I+   IDLLGINYY   
Sbjct: 241 RWDAVWNRVALDGVMRGKIPELMAERMKDF-VLP----GDEEAIR-FPIDLLGINYYS-- 292

Query: 310 RVKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYDILINIKENYGNIEC 369
           R+  K    +P   +  +   D +            W +   G+YD+L+  + +YGN   
Sbjct: 293 RMTMKHETGHPFDVWWGDAHCDRWTA--------MAWPVQPDGLYDLLMEFRRDYGNPAV 344

Query: 370 FISENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTFMDNW 429
           F++ENG   +         G +HD  R+ F+R+H+  V RA+ +G NVKGY  W+ +DN+
Sbjct: 345 FVAENGAAYDD---VVTPDGQVHDAERVAFLRDHVASVGRALADGCNVKGYLCWSLLDNF 401

Query: 430 SWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAENNGF 470
            W      R+G+V VD +  L RT K S  +   +A++  F
Sbjct: 402 EWAFGLSKRFGIVRVDYDT-LVRTPKDSYRFLSEVAKSGQF 441


Lambda     K      H
   0.321    0.140    0.446 

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: 683
Number of extensions: 48
Number of successful extensions: 6
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: 470
Length of database: 444
Length adjustment: 33
Effective length of query: 437
Effective length of database: 411
Effective search space:   179607
Effective search space used:   179607
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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