GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Amantichitinum ursilacus IGB-41

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_053935921.1 WG78_RS01020 altronate dehydratase

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



>NCBI__GCF_001294205.1:WP_053935921.1
          Length = 532

 Score =  137 bits (344), Expect = 1e-36
 Identities = 125/432 (28%), Positives = 181/432 (41%), Gaps = 50/432 (11%)

Query: 6   QQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPL--------------- 50
           Q  T EG +R DGR G  N   +  LV C +     +      PL               
Sbjct: 107 QDATFEGVVRADGRVGTANYWLIFPLVFCENRNVEHLRNALEGPLGYATQDLAAYTLALL 166

Query: 51  -DAFDDPSAEREP-----PVHLIGFPGCYPNGYAE-----KMLERLTTHPNVGAVLFVSL 99
            +    P A   P      V +I   G      A+     K+L     HPNV  +   SL
Sbjct: 167 GEEMAAPRAVTRPFANVDGVRIITHAGGCGGTRADARSLCKVLAAYADHPNVAGITVFSL 226

Query: 100 GCESMNKHYLVDVVRASGRPVE---VLTIQEKGGTRSTIQYGV--DWIRGAREQLAAQQK 154
           GC++       D ++A     +   ++  Q+K  +   +   V  D + G +   A  ++
Sbjct: 227 GCQNAQISMFQDALKARNPAFDKPCLIYEQQKWDSEDAMMKAVLQDTLNGLKAANAVTRQ 286

Query: 155 VPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKT 214
            P+ LS L IG  CGGSDG SG++ANPA+G   D ++  G   I  E  EL G E  +  
Sbjct: 287 -PVPLSALKIGVKCGGSDGFSGLSANPAMGLVSDMVVAVGGGSILAEFPELCGVEASLIE 345

Query: 215 RAARPALGDEIVACVAKAARYYSILGHGSFAV----GNADGGLTTQEEKSLGAYAKSGAS 270
           R          +  +         +G  SFA     GN   GL T   KS GA  K G S
Sbjct: 346 RCQNDDDKRRFLGMMRDFEARAQAVG-TSFAANPSPGNIRDGLITDAIKSAGAAKKGGTS 404

Query: 271 PIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGS 330
           PIV ++  G+     GL LL   P G          D   +  ++A GA+V+LF+TG G+
Sbjct: 405 PIVSVLDYGEPAARPGLSLL-CTPGG----------DVESVTGIVASGANVVLFSTGLGT 453

Query: 331 VVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGA-A 389
             G+ I PV+K+  N      L   +D D G ++ G   L EV   +FE  +  + G   
Sbjct: 454 PTGNPIVPVLKIATNTRMATRLKDMIDFDCGPVISGT-PLPEVAEGLFEMVLQTAGGRYR 512

Query: 390 SKSETLGHQEFI 401
           +K++ L   +FI
Sbjct: 513 AKADRLQQYDFI 524


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: 577
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 431
Length of database: 532
Length adjustment: 34
Effective length of query: 397
Effective length of database: 498
Effective search space:   197706
Effective search space used:   197706
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 24 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