GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Desulfotomaculum hydrothermale Lam5

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_008410930.1 DESHY_RS05080 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>NCBI__GCF_000315365.1:WP_008410930.1
          Length = 552

 Score =  250 bits (639), Expect = 1e-70
 Identities = 181/568 (31%), Positives = 290/568 (51%), Gaps = 62/568 (10%)

Query: 25  EMVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPF 84
           ++++   ++ PHR  L          A G  D++  R +    + +V+++N+++  H   
Sbjct: 4   DVMKEGLARAPHRSLLK---------ALGLLDEELSRPL----IGVVNSFNEVVPGHIHL 50

Query: 85  ERFPGLIKQALHEIGSVGQFAGGVP------AMCDGVTQGEPGMELSLASRDVIAMSTAI 138
                 +K  +       + AGG P      A+CDG+  G PGM  SLASR++IA S  I
Sbjct: 51  RDIAEAVKAGV-------RMAGGTPLEFPVIAVCDGIAMGHPGMRYSLASREIIADSIEI 103

Query: 139 ALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISNKEKAAVRQLFA 198
               + FD  + +  CDK+VPG+L+ + R  ++P V V  GPM  G    +  +V Q+F 
Sbjct: 104 MAQAHPFDGLVLIPNCDKVVPGMLMAAARL-NIPAVVVSGGPMLAGRFQNQDVSVTQMFE 162

Query: 199 E------GKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTP 252
                  G+ T EEL   E  +    G+C    TAN+   L E +G+ LPG   +   + 
Sbjct: 163 AVGAVQAGRLTPEELAELEENACPGCGSCAGMFTANSMNCLTEALGMALPGNGTIPAVSA 222

Query: 253 LRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQ 312
            R  L + A  +A  L  EN   +   +I+      N +   +A G STN  LHL AIA+
Sbjct: 223 ARRRLAKAAGLRAVALVREN---LRPRDILTMANFRNGLAVDMALGCSTNTVLHLPAIAR 279

Query: 313 AAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQT 372
            AGI+L    ++E+S   P L ++ P G+  I    AAGG+  ++++LL+ GL++ +++T
Sbjct: 280 EAGIELNLDLINEISERTPHLCKLSPAGRHHIQDLDAAGGIQAVMKELLNNGLINPNIKT 339

Query: 373 VAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNL--GRG 430
           V+G      T    LE  ++          D  ++R + +P+S+ GGL ++ GNL     
Sbjct: 340 VSG-----LTVGQLLEQAKV---------KDRQVIRSVQEPYSSTGGLAVLRGNLAPNGA 385

Query: 431 VMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRANGMPELHKL 490
           V+K +AVAPE      P R+F  + +   A  AG+++   V V+R++GP+  G P + ++
Sbjct: 386 VVKRAAVAPEMLRHTGPARVFDGEEAAITAIMAGQIKPGDVVVIRYEGPK--GGPGMREM 443

Query: 491 TPFLGVLQDRGF--KVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDG 548
                VL   G   +VAL+TDGR SGAS +  +  H+SPEA  GG +A L+DGD + +D 
Sbjct: 444 LAPTSVLAGMGLDKEVALLTDGRFSGAS-RGASIGHISPEAAEGGLIALLQDGDMIEIDI 502

Query: 549 VNGELRVLVDDAEWQARSLE----PAPQ 572
            N  L   +D+   + R LE    PAP+
Sbjct: 503 PNYRLAAKLDETVIKQR-LEAWQPPAPK 529


Lambda     K      H
   0.319    0.135    0.397 

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: 897
Number of extensions: 63
Number of successful extensions: 9
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: 608
Length of database: 552
Length adjustment: 36
Effective length of query: 572
Effective length of database: 516
Effective search space:   295152
Effective search space used:   295152
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 (21.8 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