GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Paraburkholderia bryophila 376MFSha3.1

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate H281DRAFT_00666 H281DRAFT_00666 altronate hydrolase

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>FitnessBrowser__Burk376:H281DRAFT_00666
          Length = 518

 Score =  210 bits (535), Expect = 7e-59
 Identities = 142/418 (33%), Positives = 211/418 (50%), Gaps = 38/418 (9%)

Query: 4   AAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPP 63
           AA+  T  G  R DGR   RN + V   V C+  VAR I   FR  ++    P A  + P
Sbjct: 111 AAEPATFMGIRRADGRVATRNYIGVLTSVNCSATVARAIADHFRRDVN----PHALADYP 166

Query: 64  -----VHLIGFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDV 112
                V L    GC  +   E      + L     HPN  +VLFV LGCE+   + +  V
Sbjct: 167 NVDGVVALTHGLGCGIDTLGEGLAVLRRTLAGYAVHPNFHSVLFVGLGCET---NQIAGV 223

Query: 113 VRASG----RPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTIC 168
           + ++G      +   TIQ+ GG++ TI+ G+  +          ++ P+  S L++G  C
Sbjct: 224 LESAGLKDTEQLRSFTIQDSGGSKKTIERGIAMVNEMLADANRVKREPLPASHLIVGLQC 283

Query: 169 GGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVAC 228
           GGSDG SGI+ANPA+G A D L+  G T I  ET E+ G E  +  RA   A+G++++A 
Sbjct: 284 GGSDGYSGISANPALGAAVDLLVQHGGTAILSETPEVYGAEHLLTRRAVSRAVGEKLLAR 343

Query: 229 VAKAARYYSILG---HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTG 285
           +A    Y +  G     + + GN  GGLTT  EKSLGA AK G + +V + +  +     
Sbjct: 344 IAWWEEYCARNGAALDNNPSAGNKVGGLTTILEKSLGAVAKGGTTNLVDVYQYAERIDAK 403

Query: 286 GLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCAN 345
           G   +D         G+  +S   +    +A GA++I FTTGRGS  G A SP +K+  N
Sbjct: 404 GFVFMDSP-------GYDPVSATGQ----VAAGANLICFTTGRGSAYGCAPSPSLKLATN 452

Query: 346 PATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401
            A +     DMD++ G +++G  +++E+G  +F Q +  + G  SKSE    G  EF+
Sbjct: 453 TALWERQEDDMDINCGGVIDGSASIEELGEAIFAQMLECASGVPSKSEVNGYGQSEFV 510


Lambda     K      H
   0.318    0.137    0.408 

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: 593
Number of extensions: 31
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: 431
Length of database: 518
Length adjustment: 33
Effective length of query: 398
Effective length of database: 485
Effective search space:   193030
Effective search space used:   193030
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 (21.7 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