GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Shewanella sp. ANA-3

Align xylonate dehydratase monomer (EC 4.2.1.82) (characterized)
to candidate 7024896 Shewana3_2070 dihydroxy-acid dehydratase (RefSeq)

Query= metacyc::MONOMER-20629
         (591 letters)



>FitnessBrowser__ANA3:7024896
          Length = 586

 Score =  428 bits (1101), Expect = e-124
 Identities = 244/593 (41%), Positives = 349/593 (58%), Gaps = 18/593 (3%)

Query: 1   MSNRTPRRFRSRDWFDNPDHIDMTALYLERFMNYGITPEELRSGKPIIGIAQTGSDISPC 60
           M+N+ P+  RS  WF + D      +Y     N GI PE     KP+IGI  T S+++PC
Sbjct: 10  MNNKKPKTLRSASWFGSDDKNGF--MYRSWMKNQGI-PEHHFQNKPVIGICNTWSELTPC 66

Query: 61  NRIHLDLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLSYLGLVETLHGYPID 120
           N    +L QRV++GIR+AGGIP+EFPV    E+  RP+A L RNL+ +   E + G PID
Sbjct: 67  NGHLRELAQRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAIRGNPID 126

Query: 121 AVVLTTGCDKTTPAGIMAATTVNIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAG 180
            VVL  GCDKTTPA +M A + ++P IV++GGPML+G H+ + VGSGT++W   ++  AG
Sbjct: 127 GVVLLVGCDKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELHQEYKAG 186

Query: 181 EITEEEFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYK 240
            I+   F++  A  + S G CNTMGTASTM  + E LG+SL   A IPA    R  +A+ 
Sbjct: 187 NISLAAFMNAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHM 246

Query: 241 TGQRIVDLAYDDVKPLDILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDW 300
           +G RIVD+  +D+    IL++ AF NAI + AA GGSTNA  H+ A+A   GVE++ DDW
Sbjct: 247 SGMRIVDMVKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVELSLDDW 306

Query: 301 RAAYDIPLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQG 360
           R  Y +P IVN++P+G+YL E F+ AGG PAVL +L +   L  + LTV   ++ +N++ 
Sbjct: 307 RHGYTVPTIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASLWDNVKE 366

Query: 361 RETSDREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVIGEEFRKRYLSQPGQEGVFEA 420
               ++EVI     PL E  G  VL+GNL      + +VI       +L Q         
Sbjct: 367 APCYNQEVIMSLENPLVENGGIRVLRGNL----APRGAVIKPSAASAHLMQ------HRG 416

Query: 421 RAIVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIMS 480
           +A+VF+  DDY+ RI DP L+IDE  I+V++  GP G+PG AEV NM  P  LLKKGI  
Sbjct: 417 KAVVFESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKD 476

Query: 481 LPTLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAA 540
           +  + D R SGTA    +L+ +PE+   G L+ ++ GD I +D   G     + +  + A
Sbjct: 477 MVRISDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQA 536

Query: 541 R--KQDGIPAVPATMTPWQEIYRAHASQLDTGGVLEFAVKYQDLAAKLPRHNH 591
           R  K   + ++P     +  +++ H  Q D G   +F V  +   A++P H+H
Sbjct: 537 RLAKLATVKSIPVN-GGYLSLFKEHVLQADEGCDFDFLVGCR--GAEIPAHSH 586


Lambda     K      H
   0.319    0.136    0.411 

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: 888
Number of extensions: 37
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: 591
Length of database: 586
Length adjustment: 37
Effective length of query: 554
Effective length of database: 549
Effective search space:   304146
Effective search space used:   304146
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:

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