GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacZ in Escherichia coli BW25113

Align β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized)
to candidate 17781 b3721 cryptic phospho-beta-glucosidase B (NCBI)

Query= CAZy::BAD76622.1
         (455 letters)



>FitnessBrowser__Keio:17781
          Length = 470

 Score =  416 bits (1068), Expect = e-120
 Identities = 218/462 (47%), Positives = 293/462 (63%), Gaps = 20/462 (4%)

Query: 10  PDDFLWGGAVTSFQTEGAWNEGGKGLSIVDARPI-------PK--GHSDWK-VAVDFYHR 59
           P+ FLWGGA  + Q EGAW E GKG+S  D +P        P+  G  + K VA+DFYHR
Sbjct: 5   PETFLWGGATAANQVEGAWQEDGKGISTSDLQPHGVMGKMEPRILGKENIKDVAIDFYHR 64

Query: 60  YKEDIALFKELGFTAYRTSIAWTRIFPDG-EGEPNEAGLAFYDAVFDELRANGIEPVITL 118
           Y EDIALF E+GFT  R SIAW RIFP G E EPNEAGLAFYD +FDE+   GI+P++TL
Sbjct: 65  YPEDIALFAEMGFTCLRISIAWARIFPQGDEVEPNEAGLAFYDRLFDEMAQAGIKPLVTL 124

Query: 119 YHFDLPLALAKKYNGFASRKVVDLFERYARTVFERYRGKVNYWLTFNEQNLVLEQPHLWG 178
            H+++P  L K Y G+A+R V+D FE YARTVF RY+ KV  WLTFNE N+ L  P  + 
Sbjct: 125 SHYEMPYGLVKNYGGWANRAVIDHFEHYARTVFTRYQHKVALWLTFNEINMSLHAP--FT 182

Query: 179 AICPEDEDPEAFAYRVCHNVFIAHAKAVKALREIAPEAKIGGMVTYLTTYPATCRPEDAL 238
            +   +E  EA  Y+  H+  +A A+AVKA   + PEAKIG M+     YP TC+P+D L
Sbjct: 183 GVGLAEESGEAEVYQAIHHQLVASARAVKACHSLLPEAKIGNMLLGGLVYPLTCQPQDML 242

Query: 239 ANVQAKELFIDFFFDVFARGAYPRYVTNQLEKKGICLPLEAGDEELLRSQTVDFLSFSYY 298
             ++    ++ FF DV ARG YP Y+        I + +   D E L+  TVDF+SFSYY
Sbjct: 243 QAMEENRRWM-FFGDVQARGQYPGYMQRFFRDHNITIEMTESDAEDLK-HTVDFISFSYY 300

Query: 299 QSQIVRHQEQDERIIKG----LEPNPYLPKTKWGWAIDPIGLRIALKDVYARYEMPIFIT 354
            +  V H E   +  +G    + PNP+L  ++WGW IDP+GLR+ L  ++ RY+ P+FI 
Sbjct: 301 MTGCVSHDESINKNAQGNILNMIPNPHLKSSEWGWQIDPVGLRVLLNTLWDRYQKPLFIV 360

Query: 355 ENGIGLEEELNENGTVDDDERIDYLRRHIEQMKMAMEEGVEVIGYLMWGATDLLS-SQGE 413
           ENG+G ++ +  +G++ DD RI YL  H+ Q+  A+ +GV+++GY  WG  DL+S S  +
Sbjct: 361 ENGLGAKDSVEADGSIQDDYRIAYLNDHLVQVNEAIADGVDIMGYTSWGPIDLVSASHSQ 420

Query: 414 MRKRYGVIFVNRDDENLRDLKRYKKKSFYWFQRVIRTNGEEL 455
           M KRYG I+V+RDD     L R +KKSF W+  VI+T G  L
Sbjct: 421 MSKRYGFIYVDRDDNGEGSLTRTRKKSFGWYAEVIKTRGLSL 462


Lambda     K      H
   0.321    0.140    0.430 

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: 644
Number of extensions: 34
Number of successful extensions: 8
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: 455
Length of database: 470
Length adjustment: 33
Effective length of query: 422
Effective length of database: 437
Effective search space:   184414
Effective search space used:   184414
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