Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate CA265_RS10075 CA265_RS10075 phosphate acetyltransferase
Query= metacyc::GIO2-991-MONOMER (792 letters) >FitnessBrowser__Pedo557:CA265_RS10075 Length = 695 Score = 464 bits (1194), Expect = e-135 Identities = 293/725 (40%), Positives = 427/725 (58%), Gaps = 53/725 (7%) Query: 63 LFLSDISLVGQRTPLLLGFFNYFERHLPHVGFFEPIAAEALASSELRIDRHVELVYKVFN 122 +F++ ++ + G N VG+F+PI A+ + + D HVE + F+ Sbjct: 5 IFIASAEPYTGKSVIAFGMINMLLAKTQKVGYFKPIIAQDDPNKK---DEHVEAMLDYFS 61 Query: 123 LKGDVRAMTGVQDAEA---ARMIANGQHS-ELLDKIYSQYASYKEGQDLVLVEGPGPLMG 178 L +DA A M+ + S +++ I S+Y ++ D ++EG L Sbjct: 62 LP------VKYEDAFAFTRQEMLHQSEDSGTIINTIISKYKKLEDNYDFTVIEGSDFLGE 115 Query: 179 GT----ELDAQIAAALNAPVLMTMTGQPNATVADYYNRAMVKRQVFLDHHVEVLGLVMNG 234 G E +A +A L APVL+ ++G+ N T + + A+ + FL V+VLG+V N Sbjct: 116 GMAFEFESNALMAKNLGAPVLIVVSGK-NKTASQLFKSAINIYRNFLLRDVQVLGVVANM 174 Query: 235 L-PRQSHAI---LSGQLRDKFAAAGLPFAGAIPTDIMLRNVRLDEVQTAMGAQRLYGDSL 290 + P ++ I LS QL + A IPT+ L++ + E+ A+G + L+G L Sbjct: 175 VNPEEADRIKQALSNQLPAELLIA------VIPTETGLQSPTMKEITLALGGEVLFGSEL 228 Query: 291 LTDVEFDDVVVASQRLEELLEILAERPMGRPLVVTSADRLDIVLGLLAAQLSVSGPGVAG 350 L D + D+ V + L L + + L+VT DR DI++G L A LS + P +AG Sbjct: 229 L-DNQVDNFVTGAMMLPNFLRHIKDNL----LIVTPGDRGDIIIGALQANLSANYPKIAG 283 Query: 351 ILLTQAGSARSGRNYARDTIDRIFAGLSSSGLYKGSLLPVLVTDMPLRDAIRKLDNLDAA 410 I+LT AGS + I ++ GL + ++P++ + + + + Sbjct: 284 IVLT-AGSLPD------EPIIKLIEGLQT-------IIPIIAVQKGTFETTTTIGGIHSN 329 Query: 411 ILPSSTRKISQCKRLFEQYVDANAVVARLQNMVRPNRMTPKMFMHTLKSMCNATPQHIVL 470 I + +KI+ LFE+YVD A+ ++ +TP MF + L +HIVL Sbjct: 330 ITIENKKKIAVAIELFEKYVDIKALDDKIITFSYQG-ITPHMFQYQLVKWAKRDKKHIVL 388 Query: 471 PESEDKRVLAAAADVVQRGLAKITLLGDPTTILAEAAKLGLDL--SGCNIHNPNTSDRFD 528 PE D+R+L A ++ + + ITLLGDPT I +LGL+L + IHNP S ++ Sbjct: 389 PEGNDERILKAVEKLITQDIVDITLLGDPTEITNTIKRLGLNLDTNTIKIHNPGQSAHYN 448 Query: 529 KYVDMLVEARKKKGMTREVAADTLHGDVNFFATMMIVAGDADGMVSGAVHTTASTVRPAL 588 YV+ L E RK K + E+A D + DV++F TMM+ GDADGMVSGAVHTT T+RPAL Sbjct: 449 DYVNTLHELRKAKNVNLEMARDMMT-DVSYFGTMMVYKGDADGMVSGAVHTTQHTIRPAL 507 Query: 589 QVLKS-PDTPLVSSVFIMCLPDRVVVYGDCAVNVNPSAADLAQIAITSNDTAAAFGIEPR 647 Q +K+ P +VSS+F MCLP+RV ++GDCAVN NP+A LA+IAI+S +++A FGIEPR Sbjct: 508 QFVKTKPGVSVVSSIFFMCLPERVAIFGDCAVNPNPTAQQLAEIAISSAESSAKFGIEPR 567 Query: 648 VAMLSYSTLGSGSGPDVQKVSEAVAIVKQRRPDIKVEGPIQYDAAIDPKVAAVKVQGLSE 707 +AMLSYS+ SG G DV++V EA AIVK R P++K+EGPIQYDAA+DP V K+ G SE Sbjct: 568 IAMLSYSSGTSGEGEDVERVREATAIVKARHPELKIEGPIQYDAAVDPLVGRQKLPG-SE 626 Query: 708 VAGKATVFIFPDLNTGNNTYKAVQQSTGAIAMGPVMQGLLRPVNDLSRGCTVPDIINTIC 767 VAG+A+V IFPDLNTGNNTYKAVQ+ TGA+A+GP++QGL +P+NDLSRGCTV DI NT+ Sbjct: 627 VAGRASVLIFPDLNTGNNTYKAVQRETGALAIGPMLQGLNKPINDLSRGCTVDDIFNTVV 686 Query: 768 VTSIQ 772 +T+IQ Sbjct: 687 ITAIQ 691 Lambda K H 0.320 0.134 0.376 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: 1098 Number of extensions: 55 Number of successful extensions: 9 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: 792 Length of database: 695 Length adjustment: 40 Effective length of query: 752 Effective length of database: 655 Effective search space: 492560 Effective search space used: 492560 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 CA265_RS10075 CA265_RS10075 (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.10122.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-130 421.2 0.0 2.6e-130 420.3 0.0 1.5 1 lcl|FitnessBrowser__Pedo557:CA265_RS10075 CA265_RS10075 phosphate acetyltr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS10075 CA265_RS10075 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.3 0.0 2.6e-130 2.6e-130 1 304 [] 386 689 .. 386 689 .. 0.99 Alignments for each domain: == domain 1 score: 420.3 bits; conditional E-value: 2.6e-130 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyver 67 ivlPEg++er+lkA+++l++++i++ +ll++ e++++ k ++nl+ +++++++p s + ++yv++ lcl|FitnessBrowser__Pedo557:CA265_RS10075 386 IVLPEGNDERILKAVEKLITQDIVDITLLGDPTEITNTiKRLGLNLDTNTIKIHNPGQSAHYNDYVNT 453 8**********************************998889999************************ PP TIGR00651 68 lyekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvss 135 l+e+rk+k v++++ar++++D +++++++v++g adg+vsGav+tt++t+rpalq +kt++gv++vss lcl|FitnessBrowser__Pedo557:CA265_RS10075 454 LHELRKAKNVNLEMARDMMTDVSYFGTMMVYKGDADGMVSGAVHTTQHTIRPALQFVKTKPGVSVVSS 521 ******************************************************************** PP TIGR00651 136 vfimekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvk 203 +f+m+++e+v +f+DCav+++P+a++LAeiA++sa+s ++g +ep++a+lsys+++sg+ge+ve+v+ lcl|FitnessBrowser__Pedo557:CA265_RS10075 522 IFFMCLPERVAIFGDCAVNPNPTAQQLAEIAISSAESSAKFG-IEPRIAMLSYSSGTSGEGEDVERVR 588 ******************************************.************************* PP TIGR00651 204 eAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladae 271 eA++i+k ++p+l+++G++q+DaA+ + v ++k p sevag+a v++FPdL++Gn++Yk+vqR+++a lcl|FitnessBrowser__Pedo557:CA265_RS10075 589 EATAIVKARHPELKIEGPIQYDAAVDPLVGRQKLPGSEVAGRASVLIFPDLNTGNNTYKAVQRETGAL 656 ******************************************************************** PP TIGR00651 272 aiGPilqGlakPvnDLsRGasvedivnvviita 304 aiGP+lqGl+kP+nDLsRG++v+di+n+v+ita lcl|FitnessBrowser__Pedo557:CA265_RS10075 657 AIGPMLQGLNKPINDLSRGCTVDDIFNTVVITA 689 *******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (695 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: 00:00:00.01 # Mc/sec: 19.26 // [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