GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Desulfotomaculum hydrothermale Lam5

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_008410930.1 DESHY_RS05080 dihydroxy-acid dehydratase

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>NCBI__GCF_000315365.1:WP_008410930.1
          Length = 552

 Score =  363 bits (933), Expect = e-105
 Identities = 222/546 (40%), Positives = 321/546 (58%), Gaps = 20/546 (3%)

Query: 27  HRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAEYVKKGVHEAGGLPLEFPV 86
           HRS +K  G+  +E   RP+IG+ N+++E+ P + H R++AE VK GV  AGG PLEFPV
Sbjct: 15  HRSLLKALGLLDEELS-RPLIGVVNSFNEVVPGHIHLRDIAEAVKAGVRMAGGTPLEFPV 73

Query: 87  MS------LGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAAS 140
           ++      +G   +R  ++  R + +  +E   + +P DG++L+  CDK  P +LM AA 
Sbjct: 74  IAVCDGIAMGHPGMR-YSLASREIIADSIEIMAQAHPFDGLVLIPNCDKVVPGMLMAAAR 132

Query: 141 CNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHC 200
            N+PA+ VSGGPML GRF+ +++ S T +++    V+AG +T EE  E E       G C
Sbjct: 133 LNIPAVVVSGGPMLAGRFQNQDV-SVTQMFEAVGAVQAGRLTPEELAELEENACPGCGSC 191

Query: 201 MTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVREDLTMDKILTR 260
             M TA++M  + E+LGM LP N  IPAV A R+ LA  AG R V +VRE+L    ILT 
Sbjct: 192 AGMFTANSMNCLTEALGMALPGNGTIPAVSAARRRLAKAAGLRAVALVRENLRPRDILTM 251

Query: 261 QAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLE-DWELGSNVPCLVNLQPSGEYLM 319
             F N +  + A+G STN V+HL A+A+  G+EL+L+   E+    P L  L P+G + +
Sbjct: 252 ANFRNGLAVDMALGCSTNTVLHLPAIAREAGIELNLDLINEISERTPHLCKLSPAGRHHI 311

Query: 320 EDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKVITTFAEPFKPKA 379
           +D   AGG+ AV+K+L   GL++    TV+G T+   +  A   D +VI +  EP+    
Sbjct: 312 QDLDAAGGIQAVMKELLNNGLINPNIKTVSGLTVGQLLEQAKVKDRQVIRSVQEPYSSTG 371

Query: 380 GIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDIDEHCIMVL 439
           G+AVL+GNLAPNGAV+K +A    +L+H G A VF+  E     I   +  I    ++V+
Sbjct: 372 GLAVLRGNLAPNGAVVKRAAVAPEMLRHTGPARVFDGEEAAITAI--MAGQIKPGDVVVI 429

Query: 440 KGAGPKGYPGFAEVGNMPLPKKVLQ-KGI-TDMVRISDGRMSGTAYGAVVLHVSPEAAAG 497
           +  GPKG PG  E   M  P  VL   G+  ++  ++DGR SG + GA + H+SPEAA G
Sbjct: 430 RYEGPKGGPGMRE---MLAPTSVLAGMGLDKEVALLTDGRFSGASRGASIGHISPEAAEG 486

Query: 498 GPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAPK--RGYYKLYVEHVLQA 555
           G +A +Q GDMIE+D+   RL   + +  + +R  AWQ P APK   GY   Y + V  A
Sbjct: 487 GLIALLQDGDMIEIDIPNYRLAAKLDETVIKQRLEAWQ-PPAPKVTEGYLARYAKQVSSA 545

Query: 556 DQGADL 561
            QGA L
Sbjct: 546 GQGAVL 551


Lambda     K      H
   0.318    0.135    0.401 

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: 787
Number of extensions: 32
Number of successful extensions: 6
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: 577
Length of database: 552
Length adjustment: 36
Effective length of query: 541
Effective length of database: 516
Effective search space:   279156
Effective search space used:   279156
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: 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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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