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) >lcl|FitnessBrowser__Koxy:BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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