GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Paraburkholderia bryophila 376MFSha3.1

Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate H281DRAFT_01630 H281DRAFT_01630 gluconolactonase

Query= metacyc::MONOMER-13276
         (356 letters)



>FitnessBrowser__Burk376:H281DRAFT_01630
          Length = 314

 Score =  140 bits (354), Expect = 3e-38
 Identities = 96/314 (30%), Positives = 156/314 (49%), Gaps = 31/314 (9%)

Query: 53  PRLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAG-VSIFLK 111
           PR  ++   S  +E +    +WSEGP+W  +G +LL+SD P + + +W   +G VS F +
Sbjct: 18  PRFKSLTLASASVECLYQGARWSEGPIWFGDGRYLLWSDIPNDRILRWDEASGAVSTFRQ 77

Query: 112 PSGHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKR 171
            S +A             NG      G++   +  TR + + +      +V+ D Y+GKR
Sbjct: 78  SSNNA-------------NGHTRDRQGRLVSCEHLTRRVTRTE-YDGSITVLADRYRGKR 123

Query: 172 FNSPNDLFFSKSGAVYFTDPPYGLTNLDESDIKEMNYNG-VFRL-SPDGRLDLIEAGLSR 229
           FNSPND+     G+++F+DP +G+    E + +E   +  V+R+    G + ++   +  
Sbjct: 124 FNSPNDVVVKSDGSIWFSDPTFGIDGFYEGERQESELSACVYRIDGQTGEVSVVADDILG 183

Query: 230 PNGLALSPDETKLYVSNSDRASPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDG 289
           PNGLA SPDE+ LY+  S      I  + +D +G   S   L N  +   D G  G PDG
Sbjct: 184 PNGLAFSPDESVLYIVESRGEPRKIRAFDVDLDG---SGAALSN-NRVLIDAG-PGTPDG 238

Query: 290 MNIDKQGNLF------ASAPGGIYIFAPDGECLGLISGNPGQPLSNCCFGEKGQT-LFIS 342
             +D  GNL+           G+ +F P GE +G I+    +  +N CFG + +  LF++
Sbjct: 239 FRVDVHGNLWCGWGMGTDELDGVRVFTPQGEAIGHIA--LPERCANVCFGGRHRNRLFMA 296

Query: 343 ASHNVVRVRTKTFG 356
           ASH +  +   T G
Sbjct: 297 ASHGLYSLYVNTQG 310


Lambda     K      H
   0.317    0.135    0.409 

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: 400
Number of extensions: 34
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: 356
Length of database: 314
Length adjustment: 28
Effective length of query: 328
Effective length of database: 286
Effective search space:    93808
Effective search space used:    93808
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: 49 (23.5 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