Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate H281DRAFT_05063 H281DRAFT_05063 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_05063 Length = 652 Score = 190 bits (483), Expect = 1e-52 Identities = 140/449 (31%), Positives = 211/449 (46%), Gaps = 42/449 (9%) Query: 6 MTEKILAEAAGLREVT-----PGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVW 60 + +KI+ A E T PGE R D H+ + A+ G P ++ Sbjct: 198 LVQKIIERHALETEATGDSQNPGEGAFVRADWRFIHEYYTGMASHMLH--ATFGRPLKLH 255 Query: 61 DPERIVMVFDH---------NVPANTI-GAAEFQRVTREFAREQGIVN----------IF 100 PE I+M DH ++ I R FAR+ G+ N I Sbjct: 256 SPETILMFEDHLSYSHKSELHIRNGLIPDVRALSEAHRAFARDYGLRNHGYLGENGSGIS 315 Query: 101 QNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFM 160 + + GI H ++ ER + PG ++VG DSHT GA G A G+G TDM+ F TG Sbjct: 316 EGSEGISHAMMAER-YALPGQLVVGTDSHTPHSGALGCVAFGVGTTDMSNAFITGAVRMT 374 Query: 161 VPEAMRIEVTGEPEGHVYAKDVILHIIGE--IGVDGATYRSVEFTGDTIESMDVSGRMTI 218 VPE++RI++ G V AKD+ LH++ + I + EF G I + R T+ Sbjct: 375 VPESLRIDLRGPIPAGVTAKDLTLHLLADPRIRAGAGVGKVFEFAGSAISQLTTDERTTL 434 Query: 219 CNMAVEMGAKNGIMEPNRQTLDYVRARTGREFRV---YSSDEDSQYLEDHHFDVSDLEPQ 275 NM E+G GI+ P+++T+ +++ R G +F + SD+ + Y D + L P Sbjct: 435 TNMTAELGGFTGIVAPDQETVRFLKERRGVDFEIEPWMRSDDGAPYAATIEIDCTQLSPM 494 Query: 276 VACPDDVDNVYPVHRVEG-THIDEAFLGSCTNGRYEDLKIAAEVI---GDR--RVHEDVR 329 +A P D N ++++ ID A+ GSCT G+ ED EV+ DR RV E V+ Sbjct: 495 LAAPGDPGNGIALNQLSNRPQIDIAYGGSCTAGKREDFDHYHEVLAWAADRGIRVPEHVQ 554 Query: 330 FIVSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLA-PGEVSIATTNRN 388 + + ++ +E G ++ F R GA++ P CG C G +V+I+ NRN Sbjct: 555 LFLQFGTSDVRDYCIERGYLDAFERVGAVLLQPSCGACANCGPGASTDASQVTISAINRN 614 Query: 389 FRGRMGDPASSVYLANPAVVAESAIEGVI 417 F GR G V+LA+P V SA+ G I Sbjct: 615 FSGRSG--PGKVWLASPPTVVASALAGRI 641 Lambda K H 0.320 0.137 0.408 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: 631 Number of extensions: 27 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: 428 Length of database: 652 Length adjustment: 35 Effective length of query: 393 Effective length of database: 617 Effective search space: 242481 Effective search space used: 242481 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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