Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Koxy:BWI76_RS11940 Length = 890 Score = 720 bits (1859), Expect = 0.0 Identities = 395/864 (45%), Positives = 545/864 (63%), Gaps = 40/864 (4%) Query: 33 GAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDFPWFPARVVCHDIL 87 G ++LP + +VL ENL+R + + +TA + + + + + PARV+ D Sbjct: 33 GDLSRLPKSLKVLLENLLRWQDGDSVTAEDIHALAGWLKHAHADREIAYRPARVLMQDFT 92 Query: 88 GQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDR 147 G A+VDLA +R+A+ GGD A+VNP+ P L++DHS+ V+ G D DAF +N +E Sbjct: 93 GVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFG-DDDAFEENVRLEME 151 Query: 148 RNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHA--RNG--VAFPDTLVGT 203 RN +R+ F+ W Q+AF V+P G GI HQ+NLE + + + +NG VAFPDTLVGT Sbjct: 152 RNHERYVFLRWGQQAFSRFSVVPPGTGICHQVNLEYLGRAVWSEQQNGEWVAFPDTLVGT 211 Query: 204 DSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLAL 263 DSHT ++ LGV+ GVGG+EAE+ MLG+ M +PD++G +L+GK + GITATD+VL + Sbjct: 212 DSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGFKLSGKLREGITATDLVLTV 271 Query: 264 TEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTG 323 T+ LR VV ++EF+G+G ++L L DRATI+NM+PE+GAT F ID TLDY+ LTG Sbjct: 272 TQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYGATCGFFPIDAVTLDYMRLTG 331 Query: 324 REAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVP------ 377 R EQV LVE YAK G+W + V+ TL D+ +V ++AGP P RV Sbjct: 332 RSEEQVALVEAYAKAQGMWRQPGDEPVFTSTLALDMGTVEASLAGPKRPQDRVALGDVPQ 391 Query: 378 ----TSELAA-------RGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLA 426 +SEL R I + + +PDGAV+IAAITSCTNTSNP ++AAGLLA Sbjct: 392 AFAASSELEVNHAQKDKRPIDYTLNGQQYSLPDGAVVIAAITSCTNTSNPSVLMAAGLLA 451 Query: 427 RNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGAL 486 + A +GL +PWVK SLAPGSK V YL A L P L+ LGF +VG+ CTTC G SG L Sbjct: 452 KKAVERGLKPQPWVKASLAPGSKVVSDYLAHAKLTPWLDELGFNLVGYGCTTCIGNSGPL 511 Query: 487 DPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKD 546 I++ + DL AVLSGNRNF+GRIHP K +LASPPLVVAYA+AG + D+ ++ Sbjct: 512 PDPIERAIKQGDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNLDLTRE 571 Query: 547 VLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDY-GDKV--SPL 603 LG KDG+PV L +IWPS E+ A V E FRK Y +F+ + ++ KV S Sbjct: 572 PLGTGKDGQPVYLKDIWPSGIEV-AQAVEQVSTEMFRKEYAEVFEGTAEWKAIKVDRSDT 630 Query: 604 YDWRPQSTYIRRPPYWEGALAGERTLK---GMRPLAVLGDNITTDHLSPSNAIMMDSAAG 660 YDW+ STYIR P+++ + ++ G R LA+LGD++TTDH+SP+ +I DS AG Sbjct: 631 YDWQNDSTYIRLSPFFDEMGVEPKPVEDIHGARILAMLGDSVTTDHISPAGSIKADSPAG 690 Query: 661 EYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGI 720 YL G+ DFNSY + RG+H R TFAN +++NEM V G +G + R P+ Sbjct: 691 RYLQNHGVERIDFNSYGSRRGNHEVMMRGTFANIRIRNEM--VPG--VEGGMTRHLPDTQ 746 Query: 721 VTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL 780 +++A Y + PL +IAG +YG GSSRDWAAKG RL GV ++AE FERIHR+NL Sbjct: 747 PIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDWAAKGPRLLGVRVVIAESFERIHRSNL 806 Query: 781 VGMGVLPLEFKAGENRATYGIDGTEVFDV--IGSIAPRADLTVIITRKNGERVEVPVTCR 838 +GMG+LPLEF G R T G++G E D+ + ++ P + V +TR +G + + CR Sbjct: 807 IGMGILPLEFPQGMTRKTLGLNGEERIDISNLQALQPGMTVPVTLTRADGRQEVIDCRCR 866 Query: 839 LDTAEEVSIYEAGGVLQRFAQDFL 862 +DTA E++ Y+ G+L ++ L Sbjct: 867 IDTATELTYYQNDGILHYVIRNML 890 Lambda K H 0.318 0.136 0.397 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: 1952 Number of extensions: 102 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: 867 Length of database: 890 Length adjustment: 43 Effective length of query: 824 Effective length of database: 847 Effective search space: 697928 Effective search space used: 697928 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