Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_041271928.1 DHAF_RS07465 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::Smeli:SMc02570 (247 letters) >NCBI__GCF_000021925.1:WP_041271928.1 Length = 248 Score = 232 bits (592), Expect = 5e-66 Identities = 126/248 (50%), Positives = 172/248 (69%), Gaps = 2/248 (0%) Query: 1 MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60 M LFPAIDLK+G+ VRL G ME ATVY P AR F+EQG + LHVVDL+GAFAG+ Sbjct: 1 MRLFPAIDLKEGKAVRLLQGRMEDATVYGEQPVEVARKFKEQGADSLHVVDLDGAFAGKP 60 Query: 61 VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120 VN A + +++++ VQ+GGGIRTLE IE L G++RVILGTVAVR+P LV +A ++F Sbjct: 61 VNDAVILKLIQSSGLRVQVGGGIRTLERIEELLKLGVERVILGTVAVRNPELVEKAVQRF 120 Query: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180 V +GIDAK G VAV+GWAE +E+ ++LA + + GV +++TDI RDG+L G N Sbjct: 121 EEAVVIGIDAKDGLVAVQGWAEKTEIKALDLALRMKKVGVKHLVFTDISRDGMLQGPNIQ 180 Query: 181 STLELADAVSIPVIASGGLASMDDIRRMTEPDAQ--KLEGAISGRALYDGRIDPKEALDL 238 ST+ELA + V+ASGG++ ++D+R + E + LEGAI G+ALY G EAL + Sbjct: 181 STVELARLSGLQVVASGGVSRLEDLRLLQEEANRGVSLEGAIVGKALYAGAFSLAEALRV 240 Query: 239 IREARKGK 246 + + +GK Sbjct: 241 VGQRSEGK 248 Lambda K H 0.319 0.138 0.401 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: 219 Number of extensions: 5 Number of successful extensions: 3 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: 247 Length of database: 248 Length adjustment: 24 Effective length of query: 223 Effective length of database: 224 Effective search space: 49952 Effective search space used: 49952 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: 46 (22.3 bits)
Align candidate WP_041271928.1 DHAF_RS07465 (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))
# 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/TIGR00007.hmm # target sequence database: /tmp/gapView.16117.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00007 [M=231] Accession: TIGR00007 Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase 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-86 276.1 2.0 1.4e-86 275.9 2.0 1.0 1 lcl|NCBI__GCF_000021925.1:WP_041271928.1 DHAF_RS07465 1-(5-phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_041271928.1 DHAF_RS07465 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamin # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.9 2.0 1.4e-86 1.4e-86 2 230 .. 4 236 .. 3 237 .. 0.98 Alignments for each domain: == domain 1 score: 275.9 bits; conditional E-value: 1.4e-86 TIGR00007 2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkivee 70 +PaiDlkeGk+vrl+qG+++ tvy+++p+e+a+kf+e+ga+ lHvVDLdgA++g+++n vi k++++ lcl|NCBI__GCF_000021925.1:WP_041271928.1 4 FPAIDLKEGKAVRLLQGRMEDATVYGEQPVEVARKFKEQGADSLHVVDLDGAFAGKPVNDAVILKLIQS 72 8******************************************************************** PP TIGR00007 71 levkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGW 139 ++vqvGGGiR+le++e+ll+lgvervi+gt+av+npelv++++++++ e +v+++Dak+g vav+GW lcl|NCBI__GCF_000021925.1:WP_041271928.1 73 SGLRVQVGGGIRTLERIEELLKLGVERVILGTVAVRNPELVEKAVQRFE-EAVVIGIDAKDGLVAVQGW 140 ************************************************9.99***************** PP TIGR00007 140 kekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalk 208 +ek+e+++++la +++++g++++++Tdi++dG+l+G+n++ t el++ + +v+asGGvs ed++ l+ lcl|NCBI__GCF_000021925.1:WP_041271928.1 141 AEKTEIKALDLALRMKKVGVKHLVFTDISRDGMLQGPNIQSTVELARLSGLQVVASGGVSRLEDLRLLQ 209 ********************************************************************* PP TIGR00007 209 k.....lgvkgvivGkAlyegklklke 230 + + ++g+ivGkAly g ++l e lcl|NCBI__GCF_000021925.1:WP_041271928.1 210 EeanrgVSLEGAIVGKALYAGAFSLAE 236 9999888899*************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (248 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.14 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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