Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_013403985.1 CALHY_RS10795 aconitate hydratase
Query= BRENDA::P19414 (778 letters) >NCBI__GCF_000166355.1:WP_013403985.1 Length = 643 Score = 357 bits (917), Expect = e-103 Identities = 258/720 (35%), Positives = 364/720 (50%), Gaps = 89/720 (12%) Query: 60 TYAEKILYGHLDDPHGQDIQRGVSYLKLRPDRVACQDATAQMAILQFMSAGLPQV-AKPV 118 T A+KI+ HL G+ I + +R D+ QD+T MA LQF + G+ +V K Sbjct: 4 TVAQKIIKQHL--VKGEMIPG--KEIAIRIDQTLTQDSTGTMAYLQFEAMGIDRVKTKRS 59 Query: 119 TVHCDHLIQAQVGGEKDLKRAIDLNKEVYDFLASATAKYNMGFWKPGSGIIHQIVLENYA 178 + DH Q G E N + + ++ + KY + F KPG+GI HQ+ LE +A Sbjct: 60 VAYIDHNT-LQTGPE---------NADDHLYIQTVAKKYGIYFSKPGNGICHQVHLERFA 109 Query: 179 FPGALIIGTDSHTPNAGGLGQLAIGVGGADAVDVMAGRPWELKAPKILGVKLTGKMNGWT 238 PG ++G+DSHTP AGG+G LAIG GG D M G + L PKI+ V L GK+ W Sbjct: 110 VPGQTLLGSDSHTPTAGGIGMLAIGAGGLDVAVAMGGGEYYLIMPKIVKVNLKGKLQPWV 169 Query: 239 SPKDIILKLAGITTVKGGTGKIVEYFGDGVDTFSATGMGTICNMGAEIGATTSVFPFNKS 298 S KDIIL+L TVKGG GKI EY G+GV T S TI NMGAE+GATTS+FP ++ Sbjct: 170 SAKDIILELLRRLTVKGGVGKIFEYTGEGVKTLSIPERATITNMGAELGATTSIFPSDEV 229 Query: 299 MIEYLEATGRGKIADFAKLYHKDLLSADKDAEYDEVVEIDLNTLEPYINGPFTPDLATPV 358 E+L+A GR ADF ++ D DA+YDE +EIDL++L P P +PD PV Sbjct: 230 TYEFLKAQGRE--ADFVEIL------PDPDAQYDEEIEIDLSSLVPLAACPHSPDNVVPV 281 Query: 359 SKMKEVAVANNWPLDVRVGLIGSCTNSSYEDMSRSASIVKDAAAHGLKSKTIFTVTPGSE 418 S++K + V IGSCTNSSY+D+ + A I++ + ++PGS+ Sbjct: 282 SELKGIKVDQ--------VAIGSCTNSSYKDLMKVAKILEGKT---IAEHVSLVISPGSK 330 Query: 419 QIRATIERDGQLETFKEFGGIVLANACGPCIGQWDRRDIKKGDKNTIVSSYNRNFTSRND 478 Q+ + + ++G L + G +L ACGPCIG + ++NRNF R+ Sbjct: 331 QVLSMLAQNGALASMVAAGARILECACGPCIGMGQ----APRTNGISLRTFNRNFEGRS- 385 Query: 479 GNPQTHAFVASPELVTAFAIAGDLRFNPLTDKLKDKDGNEFMLKPPHGDGLPQRGYDAGE 538 G P ++ SPE A AI G L +P T G+E ++ P + + + Sbjct: 386 GTPSAQVYLVSPETAAASAITGYLT-DPRT------LGDEPKVEMP-------KSFLVND 431 Query: 539 NTYQAPPADRSTVEVKVSPTSDRLQLLKPFKPWDGKDAKDM---PILIKAVGKTTTDHIS 595 N P + VEV P +KPF GK D+ +LIK TTDHI Sbjct: 432 NLIVPPAENPHEVEVIRGPN------IKPFP--QGKPLPDVVVGKVLIKLGDNITTDHIM 483 Query: 596 MA-GPWLKYRGHLENISNNYMIGAINAENKKANCVKNVYTGEYKGVPDTARDYRDQGIKW 654 + L YR ++ +S +Y + + PD + R+ G + Sbjct: 484 PSNAKLLPYRSNIPYLS-DYCLTPCD--------------------PDFPKRARENGGGF 522 Query: 655 VVIGDENFGEGSSREHAALEPRFLGGFAIITKSFARIHETNLKKQGLLPLNFKNPADYDK 714 +V G N+G+GSSREHAAL P +LG ++ KSFARIH NL G++P+ F+NP+DYD Sbjct: 523 IV-GGVNYGQGSSREHAALVPLYLGIKGVLAKSFARIHMANLINNGIIPMVFENPSDYDT 581 Query: 715 INPDDRIDILGLAELAPGKPVTMRVHPKNGKPWDAVLTHTFNDEQIEWFKYGSALNKIKA 774 I D + I E V + + G + +L T D Q + +G LN KA Sbjct: 582 IEEMDELKIENAREQIEKSDVLIIENVTKGLKYKMILNLT--DRQRQMILHGGLLNLTKA 639 Lambda K H 0.317 0.136 0.405 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: 1133 Number of extensions: 56 Number of successful extensions: 7 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: 778 Length of database: 643 Length adjustment: 39 Effective length of query: 739 Effective length of database: 604 Effective search space: 446356 Effective search space used: 446356 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 WP_013403985.1 CALHY_RS10795 (aconitate hydratase)
to HMM TIGR01342 (putative aconitate hydratase (EC 4.2.1.3))
# 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/TIGR01342.hmm # target sequence database: /tmp/gapView.762813.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01342 [M=655] Accession: TIGR01342 Description: acon_putative: putative aconitate hydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-296 969.4 0.1 4.6e-296 969.2 0.1 1.0 1 NCBI__GCF_000166355.1:WP_013403985.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166355.1:WP_013403985.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 969.2 0.1 4.6e-296 4.6e-296 1 647 [. 4 639 .. 4 643 .] 0.99 Alignments for each domain: == domain 1 score: 969.2 bits; conditional E-value: 4.6e-296 TIGR01342 1 tlaekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfknad 73 t+a+ki+++hlv+g++ pg+eiai+idqtl+qd+tgtm yl+fea+++d vkt+ +v yidh+tlqt nad NCBI__GCF_000166355.1:WP_013403985.1 4 TVAQKIIKQHLVKGEMIPGKEIAIRIDQTLTQDSTGTMAYLQFEAMGIDRVKTKRSVAYIDHNTLQTGPENAD 76 89*********************************************************************** PP TIGR01342 74 dhkylrsvakkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvavamageay 146 dh y+++vakkygiy+skpgngichqvh+erfa pg+tllgsdshtptagg+g+laigaggldvavam+g+ y NCBI__GCF_000166355.1:WP_013403985.1 77 DHLYIQTVAKKYGIYFSKPGNGICHQVHLERFAVPGQTLLGSDSHTPTAGGIGMLAIGAGGLDVAVAMGGGEY 149 ************************************************************************* PP TIGR01342 147 ylkmpkvvnvrlkgklpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatitnmgaelgatss 219 yl mpk+v+v+lkgkl wv+akd+ilellrrl+vkgg+gk++eytgegvk ls+peratitnmgaelgat+s NCBI__GCF_000166355.1:WP_013403985.1 150 YLIMPKIVKVNLKGKLQPWVSAKDIILELLRRLTVKGGVGKIFEYTGEGVKTLSIPERATITNMGAELGATTS 222 ************************************************************************* PP TIGR01342 220 ifpsdeitedylaafdreeefvelladadaeydevivvdlselepliaepsspdnvvpvrevegikveqvvvg 292 ifpsde+t ++l+a++re +fve+l+d+da+yde+i++dls l pl a p+spdnvvpv e++gikv+qv +g NCBI__GCF_000166355.1:WP_013403985.1 223 IFPSDEVTYEFLKAQGREADFVEILPDPDAQYDEEIEIDLSSLVPLAACPHSPDNVVPVSELKGIKVDQVAIG 295 ************************************************************************* PP TIGR01342 293 sctnsayvdllraakllegrevskdvvlivapgskqalellaregallellkagvrileaacgacigigfvpa 365 sctns+y+dl++ ak+leg+ + ++v l+++pgskq l +la++gal+ +++ag+rile+acg+cig+g +p NCBI__GCF_000166355.1:WP_013403985.1 296 SCTNSSYKDLMKVAKILEGKTIAEHVSLVISPGSKQVLSMLAQNGALASMVAAGARILECACGPCIGMGQAPR 368 ************************************************************************* PP TIGR01342 366 sdsvslrsfnrnfkgragieddkvylaspevavaaaiageivdprdlaedeglkairvemgekysygdeadid 438 ++++slr+fnrnf+gr+g++ ++vyl+spe+a+a+ai+g + dpr l ++ ++vem++++ d+ ++ NCBI__GCF_000166355.1:WP_013403985.1 369 TNGISLRTFNRNFEGRSGTPSAQVYLVSPETAAASAITGYLTDPRTLGDE-----PKVEMPKSFLVNDNLIVP 436 ***********************************************986.....899********9998887 PP TIGR01342 439 iltkeeridvelikgpnikslpvkeplgedvegevllkvednittdhiipatadilklrsniealseyvlsrv 511 + e+ +ve+i+gpnik+ p+ +pl++ v g+vl+k+ dnittdhi+p+ a++l++rsni ls+y l+ NCBI__GCF_000166355.1:WP_013403985.1 437 P--AENPHEVEVIRGPNIKPFPQGKPLPDVVVGKVLIKLGDNITTDHIMPSNAKLLPYRSNIPYLSDYCLTPC 507 5..688899**************************************************************** PP TIGR01342 512 ddefverakkldekgkagvlvagenygqgssrehaalaprflgveavlaksfarihkanlvnfgvlpleidnk 584 d++f +ra++ g +v+g nygqgssrehaal+p +lg++ vlaksfarih anl+n g++p+ ++n NCBI__GCF_000166355.1:WP_013403985.1 508 DPDFPKRARENGG----GFIVGGVNYGQGSSREHAALVPLYLGIKGVLAKSFARIHMANLINNGIIPMVFENP 576 *****99987766....******************************************************** PP TIGR01342 585 edydkielgdevevvdliealkdgeeilvvrktddeeilatldlsevekeiliaggklslikq 647 dyd ie de+++ + e++++ + ++ ++t++ + l+l+++++++++ gg l+l+k NCBI__GCF_000166355.1:WP_013403985.1 577 SDYDTIEEMDELKIENAREQIEKSDVLIIENVTKGLKYKMILNLTDRQRQMILHGGLLNLTKA 639 ***********************99888899******************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (655 nodes) Target sequences: 1 (643 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 25.70 // [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