Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 7024359 Shewana3_1551 phosphate acetyltransferase (RefSeq)
Query= BRENDA::Q8ZND6 (714 letters) >FitnessBrowser__ANA3:7024359 Length = 717 Score = 956 bits (2471), Expect = 0.0 Identities = 480/715 (67%), Positives = 589/715 (82%), Gaps = 8/715 (1%) Query: 1 MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60 MSR IMLIP GT VGLTS+SLG++RA+ER GV++ FKPI+Q R + P+++TTI+ + Sbjct: 1 MSRNIMLIPIGTGVGLTSLSLGMVRALERHGVKVQFFKPISQLRPNDNGPERSTTILSKS 60 Query: 61 STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120 T+ EP M+H E+L+ ++Q DVLME+IIA + E ++VEGLVPTR H FA Sbjct: 61 PTVNPLEPFDMAHAEALIRADQTDVLMEQIIARAAECASNTETLIVEGLVPTRNHPFADD 120 Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180 +NY IAK ++A+++F+ + G+DTP L R+E+ +S+GG N + G +INK+ APVD+ Sbjct: 121 VNYAIAKAMDADVIFIATPGSDTPTGLMNRLEIAYNSWGGKNNKRLIGAVINKIGAPVDD 180 Query: 181 QGRTRPDLSEIFDDS----SKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMAR 236 +GR RPDLSE+FD S A ++ P K SPL +LG+VP++ DL+A RA D+A+ Sbjct: 181 EGRARPDLSEVFDHQGVQRSDASIMFQMPGK----SPLRILGSVPYNLDLVAPRASDLAK 236 Query: 237 HLNATIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNG 296 HL A I+N G++ TRR++ VTFCARS+P+M+ H + SLLVTS DR DV+V+ACLAAMNG Sbjct: 237 HLRARILNAGEMNTRRLRKVTFCARSLPNMVNHIKTDSLLVTSGDRSDVIVSACLAAMNG 296 Query: 297 VEIGALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHER 356 V+IGALLLTG YE + I KLCE+AF TGLPVF+++TNTWQTSL++Q F+ EVPVDD R Sbjct: 297 VKIGALLLTGSYEPEPEILKLCEQAFETGLPVFLIDTNTWQTSLNIQRFDHEVPVDDAVR 356 Query: 357 IEKVQEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRT 416 I+ VQEYVA++++ WIES+T S R RLSPPAFRY+LTELAR A K VVLPEGDEPRT Sbjct: 357 IDLVQEYVASHIDQSWIESVTKNSPREHRLSPPAFRYKLTELARAAHKTVVLPEGDEPRT 416 Query: 417 VKAAAICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRK 476 +KAAAICAERGIA CVLLG DEI R+AA Q V LG G+ IVDP+ VR+ YV +++LR+ Sbjct: 417 IKAAAICAERGIARCVLLGKKDEIQRIAAQQDVVLGEGVVIVDPDEVRDRYVEPMLDLRR 476 Query: 477 SKGMTEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLV 536 +KG+TE VA+EQLEDN+VLGT+ML Q+EVDG+VSGAV+TTANTIRPPLQLIKTAPGSSLV Sbjct: 477 NKGLTEVVAKEQLEDNMVLGTMMLAQNEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLV 536 Query: 537 SSVFFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSG 596 SS+FFML+P+QV VYGDCAINPDP AEQLA+IAIQSA+SA AFGIEPRVAM+SYSTG SG Sbjct: 537 SSIFFMLMPDQVLVYGDCAINPDPNAEQLADIAIQSAESAKAFGIEPRVAMISYSTGNSG 596 Query: 597 AGSDVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDL 656 GSDV+KVREATR+A+EKRPDL+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVF+FPDL Sbjct: 597 TGSDVDKVREATRIAKEKRPDLVIDGPLQYDAAVMPNVARSKAPNSPVAGQATVFVFPDL 656 Query: 657 NTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711 NTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ Sbjct: 657 NTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711 Lambda K H 0.316 0.131 0.364 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: 1388 Number of extensions: 46 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: 714 Length of database: 717 Length adjustment: 39 Effective length of query: 675 Effective length of database: 678 Effective search space: 457650 Effective search space used: 457650 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 (21.6 bits) S2: 55 (25.8 bits)
Align candidate 7024359 Shewana3_1551 (phosphate acetyltransferase (RefSeq))
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.18072.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-138 444.7 0.2 1.4e-137 444.2 0.2 1.2 1 lcl|FitnessBrowser__ANA3:7024359 Shewana3_1551 phosphate acetyltr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024359 Shewana3_1551 phosphate acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.2 0.2 1.4e-137 1.4e-137 1 304 [] 406 706 .. 406 706 .. 0.96 Alignments for each domain: == domain 1 score: 444.2 bits; conditional E-value: 1.4e-137 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhkG 76 +vlPEg+e+r++kAaa++ae++ia++vll++k+e+++ + ++v l g vv++dpd +++yve + ++r++kG lcl|FitnessBrowser__ANA3:7024359 406 VVLPEGDEPRTIKAAAICAERGIARCVLLGKKDEIQRIaAQQDVVLGEG-VVIVDPDEV--RDRYVEPMLDLRRNKG 479 69*********************************99733444555444.555666655..6*************** PP TIGR00651 77 vtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCav 153 +te a+eql+D+++l++++++++e+dg+vsGav+tta+t+rp+lq+ikt++g++lvss+f+m +++vlv++DCa+ lcl|FitnessBrowser__ANA3:7024359 480 LTEVVAKEQLEDNMVLGTMMLAQNEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIFFMLMPDQVLVYGDCAI 556 ***************************************************************************** PP TIGR00651 154 avdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlve 230 ++dPnae+LA+iA+qsa+sak++g +ep+va++syst+ sg g++v+kv+eA++i+kek+pdl++dG+lq+DaA+++ lcl|FitnessBrowser__ANA3:7024359 557 NPDPNAEQLADIAIQSAESAKAFG-IEPRVAMISYSTGNSGTGSDVDKVREATRIAKEKRPDLVIDGPLQYDAAVMP 632 ************************.**************************************************** PP TIGR00651 231 kvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304 +va++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa+v+div+++++ta lcl|FitnessBrowser__ANA3:7024359 633 NVARSKAPNSPVAGQATVFVFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTA 706 ************************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (717 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15.49 // [ok]
This GapMind analysis is from Sep 17 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