Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase
Query= BRENDA::P25516 (891 letters) >FitnessBrowser__Burk376:H281DRAFT_06210 Length = 898 Score = 878 bits (2268), Expect = 0.0 Identities = 456/887 (51%), Positives = 597/887 (67%), Gaps = 29/887 (3%) Query: 12 TLQAKDKTYHYYSLPLA-AKSLGDITRLPKSLKVLLENLLRWQDGNSVTEEDIHALAGWL 70 TL+ Y L A A+ ++ LP SL++LLEN +R + G +D+ A+ WL Sbjct: 13 TLETASGPLRYADLKRAEAQGFAPLSELPVSLRILLENAMR-RGG----VDDVAAIRDWL 67 Query: 71 KNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHS 130 +DREI++ P RVLM D + VP V DLAAMR+AV++ GGD+ +VNPL PVD+V+DHS Sbjct: 68 TRRESDREISFFPVRVLMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHS 127 Query: 131 VTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGK 190 D G +AF+ N+ LE +RNHERY FLKW + AF VVPP TGI HQVNLE+L Sbjct: 128 AITDHAGRSDAFDLNLALEYQRNHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAA 187 Query: 191 AVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVV 250 V + + D PDTLVG DSHTTM+N +GVLGWGVGGIEA AA+LGQP+SML+P V+ Sbjct: 188 GVQTVVIDDVTFVVPDTLVGMDSHTTMVNSIGVLGWGVGGIEAAAAILGQPISMLLPRVI 247 Query: 251 GFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEY 310 G +++G+ R G+T TD+VL++T+ LR VVG FVEF+G+GLD+LP++DRATIANM+PE Sbjct: 248 GCRISGRPRSGVTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDRATIANMAPEA 307 Query: 311 GATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWR---NPGDEPI-FTSTLELD 366 GAT FFP DA T++Y+ +GRS +QV + E KAQG+WR +E I ++ LE D Sbjct: 308 GATMCFFPPDAATIEYLHATGRSREQVAVAEAVLKAQGIWRPEAGADEERIAYSDRLEFD 367 Query: 367 MNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQYQLPDGA 426 ++ V S+AGPKRPQDRV L DV F H+ ++ + L +G+ Sbjct: 368 LSAVTPSMAGPKRPQDRVDLKDVSARF-----------HR-----EFGLTAEGRGLTNGS 411 Query: 427 VVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYLAKAKLT 486 VVIAAITSCTNTSN ++ AGL+A+ G+K + WVK SL+PGS+VV+DYL ++ L Sbjct: 412 VVIAAITSCTNTSNARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQ 471 Query: 487 PYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRIHPLVKT 546 LD LGFNL GYGC TC G+SG L + I L V VLSGNRNFEGR HPL + Sbjct: 472 DDLDSLGFNLTGYGCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARA 531 Query: 547 NWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQVST-EM 605 N+L SP LVVAYA AG + +L +EPI + G PV L D+WP +I ++ T M Sbjct: 532 NFLGSPALVVAYACAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTM 591 Query: 606 FRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPA-PVEDIHGARI 664 F++ YA F+G A W+ I D + W + STYIR P+FD A + +I GAR Sbjct: 592 FKRVYATAFQGEARWQRIAAASGDHFDWDQASTYIRRPPYFDAGFADDGFGMANIVGARA 651 Query: 665 LAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGTFANI 724 L MLGDS+TTDHISP G I+ ++ AGR+L G GV DFN+ SRR NH+VMMRGTFAN+ Sbjct: 652 LLMLGDSITTDHISPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANV 711 Query: 725 RIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDWAAKG 784 R+RNEM P EG +RH+P DV+ ++ AA RY+ E+ PL VIAG +YG+GSSRDWAAKG Sbjct: 712 RLRNEMTPDREGPWSRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKG 771 Query: 785 PRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN-LQP 843 PRLLG+R VIAESFERIHRSNL+GMGILPL+FP G TRKTLGLTGEE I ++ LQP Sbjct: 772 PRLLGVRAVIAESFERIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEGALQP 831 Query: 844 GATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNML 890 + ++RA+G+++ + CR+D E+ +Y++ G+L Y+ +L Sbjct: 832 HQRIECEVSRANGARDSITLICRLDIPREIAWYRHGGVLQYIAAQLL 878 Lambda K H 0.317 0.135 0.401 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: 1946 Number of extensions: 90 Number of successful extensions: 8 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: 891 Length of database: 898 Length adjustment: 43 Effective length of query: 848 Effective length of database: 855 Effective search space: 725040 Effective search space used: 725040 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: 56 (26.2 bits)
Align candidate H281DRAFT_06210 H281DRAFT_06210 (aconitate hydratase)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (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/TIGR01341.hmm # target sequence database: /tmp/gapView.2627498.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01341 [M=876] Accession: TIGR01341 Description: aconitase_1: aconitate hydratase 1 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1096.5 0.0 0 1094.4 0.0 1.7 1 FitnessBrowser__Burk376:H281DRAFT_06210 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Burk376:H281DRAFT_06210 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1094.4 0.0 0 0 5 875 .. 23 877 .. 20 878 .. 0.96 Alignments for each domain: == domain 1 score: 1094.4 bits; conditional E-value: 0 TIGR01341 5 yyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqd 73 y lk++e + +s+lp slrille+++r+ +dv a+ +w + +d+ei+f p rv++ d FitnessBrowser__Burk376:H281DRAFT_06210 23 YADLKRAEAQgFAPLSELPVSLRILLENAMRRGG-----VDDVAAIRDWLTRRESDREISFFPVRVLMPD 87 677887776646789****************864.....4799*************************** PP TIGR01341 74 ftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykfl 143 + vp+v dlaa+r+av++ g+d+ ++npl+pvd+v+dhs d+ag ++a++ n+ le++rn+ery+fl FitnessBrowser__Burk376:H281DRAFT_06210 88 SSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHSAITDHAGRSDAFDLNLALEYQRNHERYAFL 157 ********************************************************************** PP TIGR01341 144 kwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGG 213 kwa++af n++vvpp+tGivhqvnle+la v + d +++ pd+lvG dshttm+n +GvlGwGvGG FitnessBrowser__Burk376:H281DRAFT_06210 158 KWAQNAFDNVRVVPPATGIVHQVNLEFLAAGVQTVVIDDVTFVVPDTLVGMDSHTTMVNSIGVLGWGVGG 227 ********************************************************************** PP TIGR01341 214 ieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladr 283 iea aa+lGqp+s+ +p viG ++ G+ r Gvt td+vl +te+lr k vvg fveffGegl++l+++dr FitnessBrowser__Burk376:H281DRAFT_06210 228 IEAAAAILGQPISMLLPRVIGCRISGRPRSGVTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDR 297 ********************************************************************** PP TIGR01341 284 atianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd..dsee..pkytdvveld 349 atianmape Gat++ffp d+ t++yl+ tgr+ ++v + e+ lkaq++++ ++e + y+d +e d FitnessBrowser__Burk376:H281DRAFT_06210 298 ATIANMAPEAGATMCFFPPDAATIEYLHATGRSREQVAVAEAVLKAQGIWRPeaGADEerIAYSDRLEFD 367 **************************************************973322224599******** PP TIGR01341 350 lsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaits 419 ls v +s+aGpkrpqdrv+lk+v a f++ +++l+ + l++g+vviaaits FitnessBrowser__Burk376:H281DRAFT_06210 368 LSAVTPSMAGPKRPQDRVDLKDVSARFHR---------EFGLT---------AEGRGLTNGSVVIAAITS 419 *************************8865.........44443.........34556899********** PP TIGR01341 420 ctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttc 489 ctntsn ++gagl+a+ G+k k +vktsl+pGs+vvtdyl esgl++ l+ lGfnl GyGc tc FitnessBrowser__Burk376:H281DRAFT_06210 420 CTNTSNARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQDDLDSLGFNLTGYGCMTC 489 ********************************************************************** PP TIGR01341 490 iGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepig 559 G sG+l+ ev+ i ++l+v++vlsGnrnfegr hpl +an+l sp lvvaya aGt+ dl++epi+ FitnessBrowser__Burk376:H281DRAFT_06210 490 AGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARANFLGSPALVVAYACAGTILRDLTTEPIA 559 ********************************************************************** PP TIGR01341 560 tdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyirep 629 + dG++v l d+wp +i+++ ++ v+ +fk+ y++ ++g++rw+++ ++s+d ++wd+ styir+p FitnessBrowser__Burk376:H281DRAFT_06210 560 DEADGQPVMLADVWPDDADIDAIFRRIVTLTMFKRVYATAFQGEARWQRIAAASGDHFDWDQASTYIRRP 629 ********************************************************************** PP TIGR01341 630 pffee.lklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGn 698 p+f+ + + + +i gar ll+lGdsittdhisp G i+ ++ a+++l+ Gv + dfn+ srr n FitnessBrowser__Burk376:H281DRAFT_06210 630 PYFDAgFADDGFGMANIVGARALLMLGDSITTDHISPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRAN 699 ***962566677999******************************************************* PP TIGR01341 699 hevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaa 768 h+vm+rGtfan+r++n++ + +eG+ ++++p ++v+ v++aa +y++e+vpl+v+aG++yG+Gssrdwaa FitnessBrowser__Burk376:H281DRAFT_06210 700 HDVMMRGTFANVRLRNEMTPDREGPWSRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAA 769 ********************************************************************** PP TIGR01341 769 kgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddie.elkpkkevtvel 837 kg++llGv+aviaesferihrsnlvgmG+lpl+f+ g++++tlgltgee + +ie l+p+++++ e+ FitnessBrowser__Burk376:H281DRAFT_06210 770 KGPRLLGVRAVIAESFERIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEgALQPHQRIECEV 839 ***************************************************999986479********** PP TIGR01341 838 vkedgeketveavlridtevelayvkkgGilqyvlrkl 875 +++g + +++ +r+d + e+a++++gG+lqy+ +l FitnessBrowser__Burk376:H281DRAFT_06210 840 SRANGARDSITLICRLDIPREIAWYRHGGVLQYIAAQL 877 *********************************97665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (876 nodes) Target sequences: 1 (898 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 21.29 // [ok]
This GapMind analysis is from Apr 09 2024. 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