Alignments for a candidate for xad in Rhizobium leguminosarum WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Rhizobium leguminosarum WSM1325

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate WP_012758573.1 RLEG_RS15645 dihydroxy-acid dehydratase

Query= reanno::pseudo5_N2C3_1:AO356_28760
         (594 letters)



>NCBI__GCF_000023185.1:WP_012758573.1
          Length = 579

 Score =  484 bits (1245), Expect = e-141
 Identities = 261/570 (45%), Positives = 359/570 (62%), Gaps = 15/570 (2%)

Query: 7   RRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLE 66
           RRLRS++W+   +      +Y   ++       +L  GRP+IGI  T SD+TPCN H  E
Sbjct: 9   RRLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65

Query: 67  LAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVLTT 126
           LA++VKAG+ +AGG P+E PV   +E + RPTA + RNLA L + E + G P+DG VL  
Sbjct: 66  LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125

Query: 127 GCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEG 186
           GCDKTTP+ +M AA+ DLP+IV++GGPML+G+ +GE +GSGT LW    ++ AGE+    
Sbjct: 126 GCDKTTPSLIMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185

Query: 187 FMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRIC 246
           F+E   + S S G CNTMGTA +M ++AEALGM+L G A+IP     R  MA  TG+RI 
Sbjct: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245

Query: 247 ELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGED 306
           ++V  D++PS+IMT+QAFENAI   +A+G S+N   HL+AIA  +G++LSLDDW R G D
Sbjct: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305

Query: 307 VPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSN 366
           VP +VN MP+GKYL E F  AGG+P V+  L +AG LH+D  TVSG T+ + V   +  N
Sbjct: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365

Query: 367 ADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIV 425
            DVI P +  L    G +VL GN     A++K S                      RA+V
Sbjct: 366 EDVILPAEKALTASGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHRGRAVV 414

Query: 426 FEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSLPCL 485
           FE  +DY A+I+D  LDIDE CI+V++  G  GYPG AEV NM  P  ++K+GI  +  +
Sbjct: 415 FEDIDDYKAKINDENLDIDETCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474

Query: 486 GDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLE 545
            D R SGT+    +L+ SPEAAVGG LA+++  D +++D+  R ++L I DEE+ARR  E
Sbjct: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAE 534

Query: 546 WTPNIPPSQTPWQELYRQLVGQLSTGGCLE 575
           W PN     + +  L++Q V    TG  L+
Sbjct: 535 WQPNHDLPTSGYAFLHQQHVEGADTGADLD 564


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: 1013
Number of extensions: 62
Number of successful extensions: 3
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: 579
Length adjustment: 37
Effective length of query: 557
Effective length of database: 542
Effective search space:   301894
Effective search space used:   301894
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 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