Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_086512002.1 BZY95_RS21875 phosphate acetyltransferase
Query= SwissProt::Q9I5A5 (704 letters) >NCBI__GCF_002151265.1:WP_086512002.1 Length = 724 Score = 806 bits (2082), Expect = 0.0 Identities = 428/707 (60%), Positives = 523/707 (73%), Gaps = 15/707 (2%) Query: 6 IAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTHGLDTP 65 + PTG GVGLTS LGL++AL+ GLK GF KP Q GP+RS+ LV T G+ P Sbjct: 15 MVPTGVGVGLTSACLGLMQALDTIGLKAGFLKPFRQDELNGPGPDRSTALVGSTLGMRPP 74 Query: 66 KPLPLAQVERMLGDGQLDELLEEIISLYQRA-----AADKDVVIVEGMVPTRHASYAARV 120 P+P A +ER+L +LD L+E++I L+ +A D+++VEG+VPT H +YA ++ Sbjct: 75 APIPQADMERLLRQDRLDVLMEQVIELFDQAMDGHDGTTPDLIVVEGVVPTAHGTYATQL 134 Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRG----- 175 N LA +L+A VILV + + L +++++ A FGG + LG IL +++ Sbjct: 135 NAQLAHALNARVILVGSGDAAAPEALAEQLDMHASAFGGVGSARTLGCILMRMQNLPGGE 194 Query: 176 EADAANAEDGVA---DFARRLTEHSPLLRDD-FRLIGCIPWQDELNAARTRDIADLLSAR 231 E A V F L HSP L D F LIG +P+ L A R D+A L AR Sbjct: 195 EPTLAPGTSSVMLDDTFLDELRRHSPALATDRFHLIGVVPYNPALIAPRVVDVARALDAR 254 Query: 232 VINAGDYEQRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAG 291 ++ GD RRV LCAR+ N + + +PG L+VT GDRDDI+LA++LA MNGVP+AG Sbjct: 255 FLHEGDAANRRVLSTSLCARSAANALHVFRPGSLIVTSGDRDDIVLASALATMNGVPMAG 314 Query: 292 LLLCSDFPPDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVT 351 +LL + F P+ ++E+CR AL+ G+PVL+V T S+ TA NL RM +IP+DD ERAE+VT Sbjct: 315 VLLTNGFMPNDNMIEMCRPALKTGMPVLAVDTDSFTTAKNLGRMGNDIPMDDLERAEQVT 374 Query: 352 EFVAGHIDFEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAI 411 FVAGH+D +WLK RLSP AFR+Q+V+ AQ+A +RI+LPEGSEPRTV+AAAI Sbjct: 375 RFVAGHLDLQWLKDHLSRGFTRRLSPSAFRHQLVKLAQRANRRIILPEGSEPRTVEAAAI 434 Query: 412 CQARGIARCVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNA 471 CQ RGIA CVLLA+ EEV+ VA+ +GI LPEGLEI+DP+ +R RYV PMVE R+GK +N Sbjct: 435 CQRRGIANCVLLARREEVEEVARNRGIELPEGLEILDPEHIRSRYVAPMVERRRGK-VNE 493 Query: 472 PMAEQQLEDSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFM 531 AE QL+D+VVL TMML LDEVDGLVSGAIHTTA+T+RPA QLIKTAPGY VSS+FFM Sbjct: 494 LTAEDQLQDNVVLGTMMLQLDEVDGLVSGAIHTTANTVRPAFQLIKTAPGYRQVSSIFFM 553 Query: 532 LLPDQVLVYGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVD 591 LLP+QV+VYGDCAVNPDP A LAEIA+QSA SAQAFGI RVAMISYSTG+SGSG DVD Sbjct: 554 LLPEQVVVYGDCAVNPDPDAEALAEIAIQSARSAQAFGIEPRVAMISYSTGESGSGADVD 613 Query: 592 KVREATRLAREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTT 651 KVR+ATRLAREQ PDLLIDGPLQYDAAAI SVGRQKAP+SPVAG+ATVF+FPDLNTGNTT Sbjct: 614 KVRQATRLAREQAPDLLIDGPLQYDAAAIESVGRQKAPDSPVAGRATVFVFPDLNTGNTT 673 Query: 652 YKAVQRSADCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698 YKAVQRSA VSVGPMLQGL KPVNDLSRGALV+DIVYTIALTAIQA Sbjct: 674 YKAVQRSARVVSVGPMLQGLNKPVNDLSRGALVDDIVYTIALTAIQA 720 Lambda K H 0.319 0.136 0.388 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: 1360 Number of extensions: 55 Number of successful extensions: 4 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: 704 Length of database: 724 Length adjustment: 39 Effective length of query: 665 Effective length of database: 685 Effective search space: 455525 Effective search space used: 455525 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: 55 (25.8 bits)
Align candidate WP_086512002.1 BZY95_RS21875 (phosphate acetyltransferase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))
# 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.carbon/TIGR00651.hmm # target sequence database: /tmp/gapView.10646.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00651 [M=304] Accession: TIGR00651 Description: pta: phosphate acetyltransferase 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-126 408.5 0.0 1.4e-126 408.1 0.0 1.1 1 lcl|NCBI__GCF_002151265.1:WP_086512002.1 BZY95_RS21875 phosphate acetyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086512002.1 BZY95_RS21875 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.1 0.0 1.4e-126 1.4e-126 1 304 [] 418 717 .. 418 717 .. 0.97 Alignments for each domain: == domain 1 score: 408.1 bits; conditional E-value: 1.4e-126 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverl 68 i+lPEgse+r+++Aaa++++++ia++vll++ ee++++ + ++++l g ++++++++ +yv + lcl|NCBI__GCF_002151265.1:WP_086512002.1 418 IILPEGSEPRTVEAAAICQRRGIANCVLLARREEVEEVaRNRGIELPEGLEILDPEHIR---SRYVAPM 483 8*********************************9998667778887776666666666...9****** PP TIGR00651 69 yekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvf 137 +e+r+ k v+e +a++ql+D+v+l++++++l+e+dglvsGa +tta+t+rpa+q+ikt++g + vss+f lcl|NCBI__GCF_002151265.1:WP_086512002.1 484 VERRRGK-VNELTAEDQLQDNVVLGTMMLQLDEVDGLVSGAIHTTANTVRPAFQLIKTAPGYRQVSSIF 551 *******.************************************************************* PP TIGR00651 138 imekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAv 206 +m ++e+v+v++DCav++dP+ae LAeiA+qsa sa+++g +ep+va++syst+ sg+g++v+kv++A+ lcl|NCBI__GCF_002151265.1:WP_086512002.1 552 FMLLPEQVVVYGDCAVNPDPDAEALAEIAIQSARSAQAFG-IEPRVAMISYSTGESGSGADVDKVRQAT 619 ****************************************.**************************** PP TIGR00651 207 kilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGP 275 ++++e++pdll+dG+lq+DaA +e+v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+a + ++GP lcl|NCBI__GCF_002151265.1:WP_086512002.1 620 RLAREQAPDLLIDGPLQYDAAAIESVGRQKAPDSPVAGRATVFVFPDLNTGNTTYKAVQRSARVVSVGP 688 ********************************************************************* PP TIGR00651 276 ilqGlakPvnDLsRGasvedivnvviita 304 +lqGl+kPvnDLsRGa+v+div+++++ta lcl|NCBI__GCF_002151265.1:WP_086512002.1 689 MLQGLNKPVNDLSRGALVDDIVYTIALTA 717 ***************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (724 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: 00:00:00.01 # Mc/sec: 19.96 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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