GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xad in Burkholderia phytofirmans PsJN

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BPHYT_RS19730 BPHYT_RS19730 dihydroxy-acid dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1668
         (594 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS19730 BPHYT_RS19730
           dihydroxy-acid dehydratase
          Length = 577

 Score =  472 bits (1214), Expect = e-137
 Identities = 265/598 (44%), Positives = 373/598 (62%), Gaps = 29/598 (4%)

Query: 2   SDTPKHRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTPC 60
           S+  K  LRS+ WF      D        +M N G+  +E   GRP+IGI  T S+LTPC
Sbjct: 4   SNQTKKPLRSQAWFG---LKDRDGFLHRSWMKNQGIPHDEFD-GRPVIGICNTWSELTPC 59

Query: 61  NRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLD 120
           N H  ELA+ VK G+ +AGG+P+EFPV  + E + RPTA L RNLA + + E + G P+D
Sbjct: 60  NAHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMD 119

Query: 121 GVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAG 180
           GV+L  GCDKTTPA LM AA+ +LPA+ +SGGPML+G  +G+ IGSGT +W     + AG
Sbjct: 120 GVILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAG 179

Query: 181 EIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYA 240
            +  E F E  +  + S GHC TMGTA +M ++ E+LGM LP  A+IPA    R  +A+ 
Sbjct: 180 TMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHL 239

Query: 241 TGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDW 300
            G+RI D+VR+D+   +I+TRQAFENAI   +A+G S+N   HLIA+A+ +GVELSLEDW
Sbjct: 240 AGRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW 299

Query: 301 QRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVS 360
           + +G +VP LVN  P+G+YL E F+ AGG+P+V+ +L + G LH++  TV+GKT+ + V 
Sbjct: 300 E-LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVR 358

Query: 361 NSLTSNTDVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSF 419
           N+   +  VI  F  P K +AG  VL GN   + A++K S    +  K            
Sbjct: 359 NAANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLK-----------H 407

Query: 420 EARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI 479
             RA+VFE  E+ HA+IDD +LDIDE CI+V++G G  GYPG AEV NM  P  ++++GI
Sbjct: 408 RGRAVVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGI 467

Query: 480 DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEM 539
             +  + DGR SGT+    +L++SPEAA GG LA ++T D +++D+  R ++L + D E+
Sbjct: 468 TDMVRISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEEL 527

Query: 540 AQRRREW-IPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGE--PRHSH 594
           A+RR  W  P  P  +  + +LY + V Q   G  L+       ++  SG   PR SH
Sbjct: 528 ARRRAAWQAPEAP--KRGYYKLYVEHVLQADQGADLD------FLVGSSGAPVPRDSH 577


Lambda     K      H
   0.319    0.135    0.407 

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: 951
Number of extensions: 58
Number of successful extensions: 4
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: 594
Length of database: 577
Length adjustment: 37
Effective length of query: 557
Effective length of database: 540
Effective search space:   300780
Effective search space used:   300780
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 (21.7 bits)
S2: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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