Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 3608667 Dshi_2060 aconitate hydratase 2 (RefSeq)
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__Dino:3608667 Length = 930 Score = 325 bits (834), Expect = 6e-93 Identities = 285/932 (30%), Positives = 431/932 (46%), Gaps = 125/932 (13%) Query: 5 YRKHVAERAAEGIAPKPLD-ANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAYV 63 Y + +A R +G+ PKP+D A + ++ +K+P L PG AA Sbjct: 7 YLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGTTSAAGA 66 Query: 64 KAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKALSH 121 KA FL I GE+ +TP+ A ELL M+GG ++ L+D DDA LA AA+ L Sbjct: 67 KAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQAAEVLKT 126 Query: 122 TLLMFDNFYDVEEKA-KAGNEYAKQVMQSWADAEWFLNRPALAEKL-TVTVFKVTGETNT 179 + +++ D + A +AGN A ++QS+A AE+F P + +++ VT G+ +T Sbjct: 127 QVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAAEGDIST 186 Query: 180 DDLSPAPDAWSRPDIPLHALAMLKNAR----EGIEPDQPGVVGPIKQIEALQQKGFPLAY 235 D LSP A SR D LH M+ A E ++ PG K++ + +KG Sbjct: 187 DLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPG-----KRVMLIAEKG----- 236 Query: 236 VGDVVGTGSSRKSATNSV-LWFMGDDIPHVPNKRGGGLCLGGK-IAPIFFNTMEDAGAL- 292 +G GSSR S N+V LW P+VP + G I+PIF T+ G + Sbjct: 237 ---TMGVGSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIG 293 Query: 293 -----------------------PIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFE 329 PI +++ G V+ + ++ + + GE LA Sbjct: 294 IDLKNWVKKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVS 353 Query: 330 LK-TDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKM 388 + ++ ++AGG ++ G+ L T A E LG+ + VF AK+++ +G + +K+ Sbjct: 354 SAFSPQAVEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKI 413 Query: 389 VGRACGVKGIRPGAYCEP------KMTSVGSQDTTGPMTRDELKDLAC--LGFSADLVMQ 440 +G+ PG ++ VGSQDTTG MT EL+ +A L + D Q Sbjct: 414 FN--ANARGVTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQ 471 Query: 441 SFCHTAA-YPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIHSW-------LNRMLLPD-T 491 S CHTA+ + NT + F+ G ++ R GV HS LN + + D Sbjct: 472 SGCHTASVWDLKAQANTPRLMA-FMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWD 530 Query: 492 VGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVH 551 + GGDSHTR G++F A SG VA A ATG + +PESV V FKGKM + RD+VH Sbjct: 531 IIIGGDSHTRMSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVH 590 Query: 552 AIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKL 611 A + Q N+F GR++E+ + L +QAF TD +AE A Sbjct: 591 ATQAQMLAQ--------HGDNVFQGRVIEVH-IGTLLADQAFTFTDWTAEMKAKASICIS 641 Query: 612 NKEPIIEYLNSNIVLLKWMIAEGY-GDRRTLERRIQGMEKWLA-----NPELLEADADAE 665 N + +IE L ++ MI +G D + L I +A L+ D A Sbjct: 642 NDDTLIESLEIAKQRIQVMIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTAR 701 Query: 666 YAAVIDIDLADIKEPILCAPN----------DPDDARPLSAVQGE-KIDEVFIGSCMTNI 714 Y A + +DL I EP++ P+ D RP+S E KID F+GSCM + Sbjct: 702 YFAEVVVDLDQIVEPMIADPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHK 761 Query: 715 GHFRAAGKL---LDAHKGQLPTR--LWVAPPTRMDAAQLTEEGYYSVFGKSGA------- 762 G + ++ L+ G++ + L +A PT +L EEG + V K Sbjct: 762 GDVKIVAQMLRNLEKANGEVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSA 821 Query: 763 -------------RIEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGANV-----F 804 +E PGC+LCMGNQ + A G TV++TSTR F R+ + Sbjct: 822 PKEKARTEYENILYLERPGCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESL 881 Query: 805 LASAELAAVAALIGKLPTPEEYQTYVAQVDKT 836 L S + ++A++G+ PT EEY+T V ++ T Sbjct: 882 LGSTPVVVLSAILGRTPTVEEYKTAVEGINLT 913 Lambda K H 0.317 0.136 0.400 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: 1706 Number of extensions: 99 Number of successful extensions: 13 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: 865 Length of database: 930 Length adjustment: 43 Effective length of query: 822 Effective length of database: 887 Effective search space: 729114 Effective search space used: 729114 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 (21.7 bits) S2: 56 (26.2 bits)
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