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

GapMind for catabolism of small carbon sources

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

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate H281DRAFT_02329 H281DRAFT_02329 dihydroxyacid dehydratase

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



>FitnessBrowser__Burk376:H281DRAFT_02329
          Length = 577

 Score =  471 bits (1213), Expect = e-137
 Identities = 266/598 (44%), Positives = 371/598 (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 GVILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKHIGSGTGVWQMSEEVRAG 179

Query: 181 EIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYA 240
            +  E F E  +  + S GHC TMGTA +M ++ E+LGM LP  A+IPA    R  +A+ 
Sbjct: 180 SMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHL 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+GKTI + V 
Sbjct: 300 E-LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHREALTVNGKTIWDNVR 358

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

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

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

Query: 540 AQRRREW-IPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGE--PRHSH 594
           A+RR  W  P  P  +  + +LY + V Q   G  L+       ++  SG   PR SH
Sbjct: 528 ARRRAAWQAPESP--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: 973
Number of extensions: 62
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 Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources