Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012116718.1 XAUT_RS24055 ATP phosphoribosyltransferase
Query= reanno::Caulo:CCNA_03626 (320 letters) >NCBI__GCF_000017645.1:WP_012116718.1 Length = 324 Score = 271 bits (694), Expect = 1e-77 Identities = 156/327 (47%), Positives = 208/327 (63%), Gaps = 11/327 (3%) Query: 1 MSTPMIFAIPSKGRLKDQVEAWLADCGFKLEMTGGARGYSAELSGLPGVSVRLLSAGDIA 60 M++P+I A+PSKGRL++ V A+ + G L GAR Y L G+ V V LSA +IA Sbjct: 1 MTSPLILAVPSKGRLQENVHAFFSRAGMPLTQARGARDYRGALGGVDNVEVAYLSASEIA 60 Query: 61 AGLDSGDLHLGVTGEDLLRERGDDMDSRVMLLRALGFGRADLVVTAPKNWLDVDTMADVD 120 A L +G H+GVTGEDL+RE + DSRV LL LGFG A++VV P+ W+DV TM D+D Sbjct: 61 AALAAGAAHIGVTGEDLVRENILEADSRVALLEKLGFGHANVVVAVPQAWIDVRTMDDLD 120 Query: 121 EVGHAHLARTGRRLRVATKYVTQTRAFFARHGVADYRIVESSGATEGAPAAGAAELVVDI 180 +V RTGRR+RVATKYV TR FFAR+G+ DYRIVES+GATEG PA+G+AEL+VDI Sbjct: 121 DVASHFHGRTGRRIRVATKYVNLTRGFFARYGIVDYRIVESAGATEGTPASGSAELIVDI 180 Query: 181 TTTGATLAANGLKILSDGVILKSQAQLTASLTAGWNGEQLDALRRLLSVVEAKGRAGKLA 240 TTTGATLAAN LK++ DG+ILKS+A L ASLTA W+G L A R + + A+ RA + Sbjct: 181 TTTGATLAANALKVVDDGIILKSEANLVASLTANWSGSALSAARAMFDRLGAEKRARTMR 240 Query: 241 TL--VWPAEQDRAAQDAVAAF--IARGGSRRANGALLATA---DLFDAAAALAEAGVEPV 293 + + + + AVA + +A G ++G L L A L E G V Sbjct: 241 EVRTRFASCDASLVEQAVARYRCVAPFGGPTSSGMLTLHCPPDTLHGLATFLREQGASMV 300 Query: 294 TVSRPDYVFESRSAVLDRFAEALKSKI 320 TV +YVF + + + EAL++++ Sbjct: 301 TVGPIEYVFAADNPLF----EALEARL 323 Lambda K H 0.318 0.133 0.375 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: 221 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: 320 Length of database: 324 Length adjustment: 28 Effective length of query: 292 Effective length of database: 296 Effective search space: 86432 Effective search space used: 86432 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: 48 (23.1 bits)
Align candidate WP_012116718.1 XAUT_RS24055 (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.4613.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-55 172.6 0.2 5.7e-55 172.1 0.2 1.3 1 lcl|NCBI__GCF_000017645.1:WP_012116718.1 XAUT_RS24055 ATP phosphoribosylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017645.1:WP_012116718.1 XAUT_RS24055 ATP phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 172.1 0.2 5.7e-55 5.7e-55 2 183 .] 6 209 .. 5 209 .. 0.94 Alignments for each domain: == domain 1 score: 172.1 bits; conditional E-value: 5.7e-55 TIGR00070 2 riAlp.KGrleeetlkllekaglklskke.erkliasaed.eevevlllrakdiptyvekgaadlGitG 67 +A+p KGrl+e++ +++++ag+ l++ + +r++ ++vev +l+a++i+ ++ gaa++G+tG lcl|NCBI__GCF_000017645.1:WP_012116718.1 6 ILAVPsKGRLQENVHAFFSRAGMPLTQARgARDYRGALGGvDNVEVAYLSASEIAAALAAGAAHIGVTG 74 69************************99999***998877368************************** PP TIGR00070 68 kDlleE....seadvvelldlgfgkcklvlAvpees.dvesledlke.........gk..riATkypnl 120 +Dl++E ++ v+ l +lgfg++++v+Avp+++ dv++++dl++ g+ r+ATky+nl lcl|NCBI__GCF_000017645.1:WP_012116718.1 75 EDLVREnileADSRVALLEKLGFGHANVVVAVPQAWiDVRTMDDLDDvashfhgrtGRriRVATKYVNL 143 ******7755555599999**********************************9984458********* PP TIGR00070 121 treylekkg.vkveivkleGavElapllgladaIvDivetGttLrengLkiiee..ilessarlia 183 tr ++++ g v+++iv++ Ga+E +p+ g a++IvDi++tG+tL++n Lk++++ il+s+a+l+a lcl|NCBI__GCF_000017645.1:WP_012116718.1 144 TRGFFARYGiVDYRIVESAGATEGTPASGSAELIVDITTTGATLAANALKVVDDgiILKSEANLVA 209 *********99*****************************************9556********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (183 nodes) Target sequences: 1 (324 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: 7.37 // [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