Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_024851287.1 N745_RS0106335 ATP phosphoribosyltransferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_3253 (211 letters) >NCBI__GCF_000526715.1:WP_024851287.1 Length = 211 Score = 262 bits (670), Expect = 3e-75 Identities = 135/207 (65%), Positives = 166/207 (80%), Gaps = 2/207 (0%) Query: 2 LTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQADVRLLIVRATDVPTYVEH 61 LTIALSKGRI DTLPLL A I+P E+P KSRKLIIPT Q +VRLLIVRATD PTYV H Sbjct: 5 LTIALSKGRIYKDTLPLLEAANILPLEDPSKSRKLIIPTNQENVRLLIVRATDAPTYVSH 64 Query: 62 GAADLGVAGKDVLMEYGGQGLYEPLDLQIARCKLMTAGKVGAPEPKG-RLRVATKFVNIA 120 GAAD+GVAGKDVLME LYE LDLQIA+C+LM AG P+P G RL++ATK++N A Sbjct: 65 GAADIGVAGKDVLMEAPSDNLYELLDLQIAKCRLMVAGP-EVPKPHGHRLKIATKYINSA 123 Query: 121 KRYYAEQGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQDFIADITSRL 180 K YYA++G QVD+IKLYGSME+APLI LADKI+D+VDTGNTL+ANGL P++ IADI+SRL Sbjct: 124 KAYYAQKGEQVDLIKLYGSMEIAPLIDLADKIVDLVDTGNTLKANGLVPEEHIADISSRL 183 Query: 181 IVNKASMKMQHARIQALIDTLRKAVES 207 IVN+ + K + +I +++ + A+ + Sbjct: 184 IVNEHAYKTKFNQIHQIVEKFKTAISN 210 Lambda K H 0.320 0.138 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: 210 Number of extensions: 6 Number of successful extensions: 1 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: 211 Length of database: 211 Length adjustment: 21 Effective length of query: 190 Effective length of database: 190 Effective search space: 36100 Effective search space used: 36100 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_024851287.1 N745_RS0106335 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))
# 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/TIGR00070.hmm # target sequence database: /tmp/gapView.6348.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00070 [M=183] Accession: TIGR00070 Description: hisG: ATP phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-57 181.1 0.0 1.2e-57 180.8 0.0 1.1 1 lcl|NCBI__GCF_000526715.1:WP_024851287.1 N745_RS0106335 ATP phosphoribosy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024851287.1 N745_RS0106335 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.8 0.0 1.2e-57 1.2e-57 1 183 [] 5 185 .. 5 185 .. 0.94 Alignments for each domain: == domain 1 score: 180.8 bits; conditional E-value: 1.2e-57 TIGR00070 1 lriAlpKGrleeetlkllekaglk.lskke.erkliasaedeevevlllrakdiptyvekgaadlGitG 67 l+iAl KGr+ ++tl lle+a++ l++++ +rkli+ +++e+v++l++ra+d ptyv++gaad+G+ G lcl|NCBI__GCF_000526715.1:WP_024851287.1 5 LTIALSKGRIYKDTLPLLEAANILpLEDPSkSRKLIIPTNQENVRLLIVRATDAPTYVSHGAADIGVAG 73 79*******************86526666689************************************* PP TIGR00070 68 kDlleEsead.vvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveiv 135 kD+l+E +d ++elldl++ kc+l++A pe + + ++ +iATky n +++y+++kg +v+++ lcl|NCBI__GCF_000526715.1:WP_024851287.1 74 KDVLMEAPSDnLYELLDLQIAKCRLMVAGPEVPKPHG-----HRLKIATKYINSAKAYYAQKGEQVDLI 137 ******76666*******************9997777.....2348*********************** PP TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183 kl+G++E+apl++lad IvD+v tG+tL++ngL+ e+i ++s+rli+ lcl|NCBI__GCF_000526715.1:WP_024851287.1 138 KLYGSMEIAPLIDLADKIVDLVDTGNTLKANGLVPEEHIADISSRLIV 185 **********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (211 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: 7.69 // [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