Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate AO353_21605 AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:B2V844 (431 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21605 Length = 866 Score = 107 bits (266), Expect = 2e-27 Identities = 127/473 (26%), Positives = 196/473 (41%), Gaps = 63/473 (13%) Query: 2 GMTITEKIIAAHAGRDYVEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPNKIA 61 G T+ +K++ G V PG K+ + D T P+ +L+ D Sbjct: 381 GFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPMTRDELK----DLACLGFSTD 436 Query: 62 LVMDHF-----FP-PKDIMSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGFVVP 115 LVM F +P P D+ + + DF G + G G++H+ L ++P Sbjct: 437 LVMQSFCHTAAYPKPIDVTTHHTLP---DFIMTRGGVSLRPGD--GIIHSWLNR--MLLP 489 Query: 116 GDLVIGADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPESMKFVFYNKPQKWVGG 175 + G DSHT GI S GS +A+ ATG L +PES+ F K Q V Sbjct: 490 DTVGTGGDSHTRFPMGI---SFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMQPGVTL 546 Query: 176 KDFV-----------LTVIGKIGVDGALY-KAMEYQGEAIRALDIDNRLTIANMAIEAGG 223 +D V L + K G A + +E +G +++ L+ A+ A G Sbjct: 547 RDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASAERSAAG 606 Query: 224 ------KSGIIEPDEKTVDWVRKRTNREF--------------------KLYKSDPDAKY 257 K I E + +R + +L +D DA+Y Sbjct: 607 CTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAMEAWIANPELMVADADAEY 666 Query: 258 CCEYEFDASKI-EPVVACPSLPSNVKPVSEVAGTHIDQVFIGSCTNGRLSDLRIAAAILK 316 E D + I EPV+ P+ P + + +S VAG ID+VFIGSC + R A +L Sbjct: 667 AEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMT-NIGHFRAAGKLLD 725 Query: 317 SKKVHPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTCGPCLGGHMGILAEGEV 376 K R + P + Q EG I AG + C C+G + V Sbjct: 726 QVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTV 785 Query: 377 CLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHPDEVAKY-EEVETL 428 +STS RNF R+G + VYL+S +A+ +++LGR+ +E Y +E++T+ Sbjct: 786 -VSTSTRNFPNRLG-DGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTM 836 Lambda K H 0.319 0.137 0.407 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: 843 Number of extensions: 43 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 431 Length of database: 866 Length adjustment: 37 Effective length of query: 394 Effective length of database: 829 Effective search space: 326626 Effective search space used: 326626 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 (21.7 bits) S2: 53 (25.0 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