Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_013430210.1 CALKRO_RS06285 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE
Query= metacyc::HISTCYCLOPRATPPHOS (203 letters) >NCBI__GCF_000166775.1:WP_013430210.1 Length = 205 Score = 152 bits (383), Expect = 5e-42 Identities = 80/194 (41%), Positives = 118/194 (60%), Gaps = 6/194 (3%) Query: 16 DGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSGNFLNVV 75 +GL+PV+VQ +GEVLML YMN EAL+ T+++G + +FSR++ ++W KGETSGN + Sbjct: 12 NGLVPVVVQDNSTGEVLMLAYMNKEALELTIQTGYMHYFSRSRNKIWRKGETSGNVQKLK 71 Query: 76 SIAPDCDNDTLLVLANPIGPTCHKGTSSCF-----GDTAHQWL-FLYQLEQLLAERKSAD 129 S+ DCD DTLL + G CH G +CF GD +++L + + +RK Sbjct: 72 SLFLDCDGDTLLAIVEQTGVACHTGNKTCFFTALEGDKKKVATDIIFELMKTINDRKQNK 131 Query: 130 PETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQGL 189 E SYT+ L+ G +I +K+GEE E + A + E+ E SDLMYHL VLL L Sbjct: 132 VEGSYTSYLFEKGLDKILKKIGEEATEVVIGAKNGKKEEVIYEISDLMYHLSVLLAYFNL 191 Query: 190 DLTTVIENLRKRHQ 203 D T ++++L +R + Sbjct: 192 DWTDILKSLEERRK 205 Lambda K H 0.317 0.132 0.384 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: 124 Number of extensions: 9 Number of successful extensions: 2 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: 203 Length of database: 205 Length adjustment: 21 Effective length of query: 182 Effective length of database: 184 Effective search space: 33488 Effective search space used: 33488 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: 45 (21.9 bits)
Align candidate WP_013430210.1 CALKRO_RS06285 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR03188.hmm # target sequence database: /tmp/gapView.1077337.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03188 [M=84] Accession: TIGR03188 Description: histidine_hisI: phosphoribosyl-ATP diphosphatase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-35 107.8 0.3 2.6e-35 106.8 0.3 1.5 1 NCBI__GCF_000166775.1:WP_013430210.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430210.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 106.8 0.3 2.6e-35 2.6e-35 3 84 .] 119 200 .. 117 200 .. 0.98 Alignments for each domain: == domain 1 score: 106.8 bits; conditional E-value: 2.6e-35 TIGR03188 3 eLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVllaekgv 75 eL ++i++rk+++ e+Syt++l+ekg dkilkK+gEEa+Ev+i akn++kee+++E++Dl+Yhl Vlla+ ++ NCBI__GCF_000166775.1:WP_013430210.1 119 ELMKTINDRKQNKVEGSYTSYLFEKGLDKILKKIGEEATEVVIGAKNGKKEEVIYEISDLMYHLSVLLAYFNL 191 799********************************************************************** PP TIGR03188 76 sledvlaeL 84 ++ d+l++L NCBI__GCF_000166775.1:WP_013430210.1 192 DWTDILKSL 200 ******987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (84 nodes) Target sequences: 1 (205 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 17.91 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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:
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