Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate RR42_RS24175 RR42_RS24175 isopropylmalate isomerase
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__Cup4G11:RR42_RS24175 Length = 469 Score = 208 bits (529), Expect = 3e-58 Identities = 145/443 (32%), Positives = 223/443 (50%), Gaps = 56/443 (12%) Query: 26 VDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFDHNVPPNTVK---AAEMQKLALEFV 82 +D + ++ T+P A++ L+ VW + DHNVP A + KL ++ + Sbjct: 27 IDRHLLNEVTSPQAFEGLRMSEHPVWRISANLAVSDHNVPTTNRSQGIADPVSKLQVDTL 86 Query: 83 KR----FGIKNFHKGG--EGICHQILAEN-YVLPNMFVAGGDSHTCTHGAFGAFATGFGA 135 FGI F +GI H I E LP M V GDSHT THGAFGA A G G Sbjct: 87 DANCDSFGITQFKMNDHRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGT 146 Query: 136 TDMAYIYATGETWIKVPKTIRVDIVGK-NENVSAKDIVLRVCKEIGRRGATYMAIEYGGE 194 +++ ++ AT K + V + GK +AKDIVL + +IG G T IE+ G Sbjct: 147 SEVEHVMATQTLLGKKTMNMLVKVEGKLPRGCTAKDIVLAIIGKIGTAGGTGNTIEFAGS 206 Query: 195 VVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDYLK---------------------- 232 ++++ ++GR+T+CNMAIE G + G++ D++T +Y K Sbjct: 207 AIRDLTVEGRMTVCNMAIEAGARAGLVAVDDVTLEYFKGRPYAPQGVEWDQAVGYWRTLH 266 Query: 233 KERGLSDEDIAKLKKERITVNRDEANYYKEIEIDITDMEEQVAVPHHPDN---------- 282 + G + + +L+ E I R + + E+ + +E++V P + Sbjct: 267 SDAGAKFDLVVELRAEEI---RPQVTWGTSPEM-VISIEDRVPDPDKEKDPNKRTAMERA 322 Query: 283 -----VKPISDVEGTEINQVFIGSCTNGRLSDLREAAKYLK--GREVHKDVKL-IVIPAS 334 ++P VE I++VFIGSCTN R+ D+R AA ++ GR+V +VKL +V+P S Sbjct: 323 LEYMGLQPNVPVESINIDKVFIGSCTNSRIDDMRAAAWVVQKLGRKVASNVKLALVVPGS 382 Query: 335 KKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAEGEICLSTTNRNFKGRMGHI 394 V QA +EG+ ++F AG PGC CL + L GE C ST+NRNF+GR G Sbjct: 383 GLVKEQAEREGLDEVFKAAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQG-A 441 Query: 395 NSYIYLASPKIAAISAVKGYITN 417 +L SP +AA +A++G+ + Sbjct: 442 GGRTHLVSPAMAAAAAIEGHFVD 464 Lambda K H 0.318 0.136 0.399 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: 467 Number of extensions: 18 Number of successful extensions: 5 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: 420 Length of database: 469 Length adjustment: 32 Effective length of query: 388 Effective length of database: 437 Effective search space: 169556 Effective search space used: 169556 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: 51 (24.3 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