GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Caldicellulosiruptor hydrothermalis 108

Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate WP_013289899.1 CALHY_RS10305 class II fructose-1,6-bisphosphate aldolase

Query= SwissProt::P42420
         (290 letters)



>NCBI__GCF_000166355.1:WP_013289899.1
          Length = 323

 Score =  207 bits (526), Expect = 3e-58
 Identities = 121/313 (38%), Positives = 181/313 (57%), Gaps = 31/313 (9%)

Query: 1   MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60
           M  V+ +E+ + A   +YAIG FN+N ++  + I++AA++EQ+P+I   S     Y    
Sbjct: 1   MPLVTTREMFKKAAEGKYAIGAFNVNNMEIIQGIVEAAKEEQAPLILQVSAGARKYAKHI 60

Query: 61  KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMT 120
             I  +V A +ED    +P+ LHLDHG   E C+  ID GF+SVMIDGS  P +ENIA+T
Sbjct: 61  YLIK-LVEAALEDSG-DLPIALHLDHGEDFEICKACIDGGFTSVMIDGSRLPFEENIALT 118

Query: 121 KEVTDYAAKHGVSVEAEVGTVGGMEDGLVGG---VRYADITECERIVKETNIDALAAALG 177
           K+V +YA + GV VEAE+G + G+ED +        + D  +    V+ T +D+LA A+G
Sbjct: 119 KKVVEYAHERGVVVEAELGKLAGIEDNVKVAEHEAAFTDPDQAAEFVERTGVDSLAVAIG 178

Query: 178 SVHG--KYQGEPNLGFKEMEAISRM--TDIPLVLHGAS---------------------G 212
           + HG  K++G+P L F+ ++ I      D P+VLHGAS                     G
Sbjct: 179 TSHGAYKFKGDPRLDFERLQKIVEKLPKDFPIVLHGASTVLPEFVEMCNKYGGNIPGAKG 238

Query: 213 IPQDQIKKAITLGHAKININTECMVAWTDETRRMFQENSDLYEPRGYLTPGIEAVEETVR 272
           +P+D ++KA  LG  KINI+T+  +A T   R+   E+ D ++PR YL  G +A++E V+
Sbjct: 239 VPEDMLRKAAELGVRKINIDTDLRLAMTAAIRKHLYEHPDHFDPRQYLKDGRDAIKEMVK 298

Query: 273 SKMRE-FGSAGKA 284
            K+R   G AGKA
Sbjct: 299 HKLRNVLGCAGKA 311


Lambda     K      H
   0.316    0.132    0.372 

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: 235
Number of extensions: 13
Number of successful extensions: 5
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: 290
Length of database: 323
Length adjustment: 27
Effective length of query: 263
Effective length of database: 296
Effective search space:    77848
Effective search space used:    77848
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 (21.6 bits)
S2: 48 (23.1 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