GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Halococcus hamelinensis 100A6

Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate WP_007690272.1 C447_RS01785 galactonate dehydratase

Query= SwissProt::Q1NAJ2
         (403 letters)



>NCBI__GCF_000336675.1:WP_007690272.1
          Length = 384

 Score =  219 bits (558), Expect = 1e-61
 Identities = 134/412 (32%), Positives = 216/412 (52%), Gaps = 37/412 (8%)

Query: 1   MPKIIDAKVIITCPGRNFVTLKIMTDEGVYGLGDATLNGRELAVASYLTDHVIPCLIGRD 60
           M +I+D ++    P   ++ L++ T +G+ G G+  + GR   VA+ + + +   L+GRD
Sbjct: 1   MTEIVDYELYDVPP--RWLFLELETSDGLVGWGEPVVEGRSKTVAAAVEELLDNYLLGRD 58

Query: 61  AHRIEDLWQYLYKGAYWRRGPVTMTAIAAVDMALWDIKGKIAGLPVYQLLGGASREGVMV 120
            +RIED WQ +Y+G ++R GP+ M+AIA +D ALWDIKGK  G PV++LLGG +R+ + V
Sbjct: 59  PNRIEDHWQAMYRGGFYRGGPILMSAIAGIDQALWDIKGKRFGAPVHELLGGRARDRIRV 118

Query: 121 YGHANGTTIEDTVKVALDYQAQGYKAIRLQCGVPGMASTYGVSKDKYFYEPADADLPTEN 180
           Y    G    D  + A +    G+ A+++              + +    PA  +   E 
Sbjct: 119 YQWIGGDRPADVGEAAAEQVEAGFSALKMN----------ATPEIRRVDSPAAVEAAVER 168

Query: 181 IWNTSKYLRIVPELFKAARESLGWDVHLLHDIHHRLTPIEAGRLGQDLEPYRPFWLEDAT 240
           +              ++ RE++G +V +  D H R+T   A RL   LEP+ P ++E+  
Sbjct: 169 L--------------RSVREAVGPEVEIGVDFHGRVTKPMAKRLVAALEPHEPMFVEEPV 214

Query: 241 PAENQEAFRLIRQHTTAPLAVGEIFNSIWDAKDLIQNQLIDYIRATVVHAGGITHLRRIA 300
             ++ +A   I  HTT P+A GE   S WD K++ ++  +D I+  + HAGGIT +++IA
Sbjct: 215 LPQHNDALAEIASHTTTPIATGERMFSRWDYKEVFEDGTVDVIQPDLSHAGGITEVKKIA 274

Query: 301 ALADLYQIRTGCHGATDLSPVCMAAALHFDLSVPNFGIQEYMR--HMPETDAVF-----P 353
           A+A+ Y +    H    L PV +A+ +  D   PN  IQE     H  ET  V      P
Sbjct: 275 AMAEAYDVALAPH--CPLGPVALASCIQVDACSPNALIQEQSLNIHYNETSDVLDYLADP 332

Query: 354 HAYTFADGMMHPGDQPGLGVDIDEDL--AAGYEYKRAFLPVNRLEDGTMFNW 403
             + + DG +   D+PGLG+D+DE+   A   E      P+ R +DG++  W
Sbjct: 333 SVFEYEDGFVDVLDEPGLGIDLDEEYIEAQSEEPVDWHNPIWRHDDGSVAEW 384


Lambda     K      H
   0.322    0.139    0.438 

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: 446
Number of extensions: 17
Number of successful extensions: 4
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: 403
Length of database: 384
Length adjustment: 31
Effective length of query: 372
Effective length of database: 353
Effective search space:   131316
Effective search space used:   131316
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 (21.9 bits)
S2: 50 (23.9 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