GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Desulfotomaculum hydrothermale Lam5

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate WP_008410930.1 DESHY_RS05080 dihydroxy-acid dehydratase

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



>NCBI__GCF_000315365.1:WP_008410930.1
          Length = 552

 Score =  289 bits (740), Expect = 2e-82
 Identities = 199/548 (36%), Positives = 285/548 (52%), Gaps = 27/548 (4%)

Query: 35  GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94
           G+  EEL   RP+IG+  + +++ P + H  ++A+ VKAG+R AGG P+EFPV  + +  
Sbjct: 23  GLLDEELS--RPLIGVVNSFNEVVPGHIHLRDIAEAVKAGVRMAGGTPLEFPVIAVCDGI 80

Query: 95  RRPTAALDRNLAYLGLV----EIL-HGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149
                 +  +LA   ++    EI+   +P DG+VL   CDK  P  LMAAA  ++PA+V+
Sbjct: 81  AMGHPGMRYSLASREIIADSIEIMAQAHPFDGLVLIPNCDKVVPGMLMAAARLNIPAVVV 140

Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209
           SGGPML G  + + + S T ++ A   + AG +  E   E+   A P  G C  M TA S
Sbjct: 141 SGGPMLAGRFQNQDV-SVTQMFEAVGAVQAGRLTPEELAELEENACPGCGSCAGMFTANS 199

Query: 210 MNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIA 269
           MN L EALGM+LPG  +IPA    R ++A A G R   LV +++RP  I+T   F N +A
Sbjct: 200 MNCLTEALGMALPGNGTIPAVSAARRRLAKAAGLRAVALVRENLRPRDILTMANFRNGLA 259

Query: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGG 329
           V  ALG S+N   HL AIAR  G+EL+LD    I E  P L    PAG++  +    AGG
Sbjct: 260 VDMALGCSTNTVLHLPAIAREAGIELNLDLINEISERTPHLCKLSPAGRHHIQDLDAAGG 319

Query: 330 VPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLKHRAGFIVLSGN 389
           + +VM EL   G ++ +  TVSG T+G+++  +   +  VI     P     G  VL GN
Sbjct: 320 IQAVMKELLNNGLINPNIKTVSGLTVGQLLEQAKVKDRQVIRSVQEPYSSTGGLAVLRGN 379

Query: 390 FF-DSAIMKMSVVG-EAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERC 447
              + A++K + V  E  R T              A VF+G E     I   A  I    
Sbjct: 380 LAPNGAVVKRAAVAPEMLRHT------------GPARVFDGEEAAITAI--MAGQIKPGD 425

Query: 448 ILVIRGVGTVGYPGSAEVVNMAPPAALIKQGID-SLPCLGDGRQSGTSASPSILNMSPEA 506
           ++VIR  G  G PG  E+  +AP + L   G+D  +  L DGR SG S   SI ++SPEA
Sbjct: 426 VVVIRYEGPKGGPGMREM--LAPTSVLAGMGLDKEVALLTDGRFSGASRGASIGHISPEA 483

Query: 507 AVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVG 566
           A GG +ALLQ  D +++D+    +   +D+  + +R   W P  P     +   Y + V 
Sbjct: 484 AEGGLIALLQDGDMIEIDIPNYRLAAKLDETVIKQRLEAWQPPAPKVTEGYLARYAKQVS 543

Query: 567 QLSTGGCL 574
               G  L
Sbjct: 544 SAGQGAVL 551


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: 867
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 594
Length of database: 552
Length adjustment: 36
Effective length of query: 558
Effective length of database: 516
Effective search space:   287928
Effective search space used:   287928
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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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