Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate N515DRAFT_2933 N515DRAFT_2933 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= ecocyc::PRIBFAICARPISOM-MONOMER (245 letters) >FitnessBrowser__Dyella79:N515DRAFT_2933 Length = 242 Score = 218 bits (555), Expect = 9e-62 Identities = 117/241 (48%), Positives = 156/241 (64%), Gaps = 4/241 (1%) Query: 2 IIPALDLIDGTVVRLHQGDYGKQRDYGNDPLPRLQDYAAQGAEVLHLVDLTGAKDPAKRQ 61 +IPA+DL G VVRL QGDYG+Q Y +P + YA GA LH+VDL GA+ + Sbjct: 5 VIPAIDLRTGRVVRLRQGDYGQQTTYEFEPRELARRYAEAGAAWLHVVDLDGARSGSLDN 64 Query: 62 IPLIKTLVAGVNVPVQVGGGVRSEEDVAALLEAGVARVVVGSTAVKSQDMVKGWFERFGA 121 + +I+ L A + VQ GGGVRSE D+ L +AGVARVVVGS A++ +V W +FG Sbjct: 65 LQVIEAL-ARDGMQVQAGGGVRSEADLQRLFDAGVARVVVGSVAIREPALVGAWLGKFGT 123 Query: 122 DALVLALDVR-IDEQGNKQVAVSGWQENSGVSLEQLVETYLPVGLKHVLCTDISRDGTLA 180 D L +ALD R ID G + +GW E SL++L Y G +H+LCTDI RDG LA Sbjct: 124 DKLTVALDTRRID--GRWALPSAGWTELEARSLDELAPWYAARGARHLLCTDIDRDGMLA 181 Query: 181 GSNVSLYEEVCARYPQVAFQSSGGIGDIDDVAALRGTGVRGVIVGRALLEGKFTVKEAIA 240 G N+ LY ++ P +A Q+SGG+ +DD+ A R G +GVI+GRALLEG+FT++EA+A Sbjct: 182 GFNLELYRDLARTAPTLAVQASGGVRSVDDIVAARAAGAQGVILGRALLEGRFTIEEALA 241 Query: 241 C 241 C Sbjct: 242 C 242 Lambda K H 0.318 0.137 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: 174 Number of extensions: 6 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: 245 Length of database: 242 Length adjustment: 24 Effective length of query: 221 Effective length of database: 218 Effective search space: 48178 Effective search space used: 48178 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate N515DRAFT_2933 N515DRAFT_2933 ( 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.4367.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-74 235.6 0.0 3.1e-74 235.5 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 N515DRAFT_2933 1-(5-phosphoribo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 N515DRAFT_2933 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylide # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.5 0.0 3.1e-74 3.1e-74 1 231 [] 5 239 .. 5 239 .. 0.97 Alignments for each domain: == domain 1 score: 235.5 bits; conditional E-value: 3.1e-74 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikk 66 +iPaiDl+ G+vvrl qGd++++t+y+ +p e+a++++e ga +lHvVDLdgA++g+ +nl+vi+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 5 VIPAIDLRTGRVVRLRQGDYGQQTTYEFEPRELARRYAEAGAAWLHVVDLDGARSGSLDNLQVIEA 70 89**************************************************************** PP TIGR00007 67 iveelevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakeg 132 ++++ ++vq GGG+Rs +++++l+++gv+rv++g++a+++p+lv +l ++g++k++v+lD+++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 71 LARD-GMQVQAGGGVRSEADLQRLFDAGVARVVVGSVAIREPALVGAWLGKFGTDKLTVALDTRRI 135 **76.67********************************************************987 PP TIGR00007 133 ....evavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvke.aevevi 193 + GW+e + sl ela ++ g++++++Tdi++dG+l+G+n+el+++l+++ + v+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 136 dgrwALPSAGWTELEARSLDELAPWYAARGARHLLCTDIDRDGMLAGFNLELYRDLARTaPTLAVQ 201 77778889*************************************************9999***** PP TIGR00007 194 asGGvssiedvkalkklgvkgvivGkAlyegklklkea 231 asGGv+s++d+ a++++g++gvi+G+Al+eg+++++ea lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 202 ASGGVRSVDDIVAARAAGAQGVILGRALLEGRFTIEEA 239 **********************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (242 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.74 // [ok]
This GapMind analysis is from Apr 09 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