GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate Echvi_3632 Echvi_3632 Altronate dehydratase

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



>FitnessBrowser__Cola:Echvi_3632
          Length = 548

 Score =  146 bits (369), Expect = 1e-39
 Identities = 101/322 (31%), Positives = 155/322 (48%), Gaps = 19/322 (5%)

Query: 88  HPNVGAVLFVSLGCESMNKHYL---VDVVRAS-GRPVEVLTIQEKGGTRSTIQYGVDWIR 143
           +PNV     +SLGC++     L   +D +     +PV +L  Q++G   + +   +    
Sbjct: 230 NPNVAGATILSLGCQNAQPSILREKLDKINPDLKKPVIILEQQQEGTENTLLTNAIQKTF 289

Query: 144 GAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETG 203
            A       ++ P  LS+L +G  CGGSDG SGI+ANP+VG A D ++  G   I  E  
Sbjct: 290 LALTDADQLERQPAPLSKLTVGLECGGSDGFSGISANPSVGHASDLVVALGGKTILSEFP 349

Query: 204 ELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHG---SFAVGNADGGLTTQEEKS 260
           EL G E  +  R       D+ V  +   A     +G G   + + GN   GL T   KS
Sbjct: 350 ELCGVEQELINRCTTDESADKFVTLMRAYAASAEAVGSGFDMNPSPGNIKDGLITDAMKS 409

Query: 261 LGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAH 320
            GA  K G SPIV ++   +     GL LL   P           +D      +   GA+
Sbjct: 410 AGAAKKGGTSPIVDVLDYAEYVTKPGLNLL-CTPG----------NDVESTTAMAGSGAN 458

Query: 321 VILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQ 380
           VILFTTG G+  G+ ++PV+KV +N      +   +D++ G ++ G  T+D++G E+ E 
Sbjct: 459 VILFTTGLGTPTGNPVTPVLKVSSNHILAEKMDDIIDINTGGVISGDKTIDQMGEEILEH 518

Query: 381 TVAVSRG-AASKSETLGHQEFI 401
            + V+ G   +K+ TL   +FI
Sbjct: 519 IIEVASGNKKAKAMTLNQDDFI 540


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: 576
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 431
Length of database: 548
Length adjustment: 34
Effective length of query: 397
Effective length of database: 514
Effective search space:   204058
Effective search space used:   204058
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: 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