Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF2655 HP15_2599 isopropylmalate isomerase large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__Marino:GFF2655 Length = 469 Score = 199 bits (506), Expect = 1e-55 Identities = 142/444 (31%), Positives = 213/444 (47%), Gaps = 62/444 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVP-----------ANTI 78 +D + H+ T+P + F + S G + W V V DH VP A+ + Sbjct: 28 IDRHLLHEVTTP---QAFSGLRSAG--RKPWRIPANVAVPDHAVPTRKRELGVAGIADRV 82 Query: 79 GAAEFQRVTREFAREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAF 136 + + ++R E GI + + GI H V PE+G PGM IV DSHT T+GAF Sbjct: 83 ARKQVETLSRN-CEEFGIPLIELEDARQGIVHVVGPEQGLTLPGMTIVCGDSHTSTHGAF 141 Query: 137 GAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGAT 196 A G+G +++ V AT + MR+ G+P V KD+IL +IG IG G Sbjct: 142 ATLAMGIGTSEVEHVLATQTLRTQKQKNMRVVFEGQPGFGVTPKDLILALIGRIGTAGGN 201 Query: 197 YRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRART---------- 246 ++E+ G I ++ + GRMTICNM++E GA+ G++ +R T YV R Sbjct: 202 GYAIEYAGAAIRNLSMEGRMTICNMSIEAGARAGMVAYDRVTEQYVEGRPQAPVGERLEQ 261 Query: 247 GREF-RVYSSDEDSQYLEDHHFDVSDLEPQVA--------------CPD----------- 280 RE+ R SD ++ + + HF + L PQV PD Sbjct: 262 AREYWRTLVSDAEADFDREEHFPLEALVPQVTWGTSPEMVTGIDGKTPDLSQLAPEKRES 321 Query: 281 -----DVDNVYPVHRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVR-FIVSP 334 D + P ++G ID+ F+GSCTN R EDL+ A ++ ++VH V+ ++ P Sbjct: 322 ARRALDYMGLEPGRPLKGLSIDKVFIGSCTNARMEDLRAVANLVQGQKVHRSVKQALIVP 381 Query: 335 ASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMG 394 S ++ L+A +G+ F AG GC CLG + L PGE +T+NRNF GR G Sbjct: 382 GSGQVRLQAEREGLDMIFRNAGFEWRAAGCSMCLGMNDDRLNPGERCASTSNRNFEGRQG 441 Query: 395 DPASSVYLANPAVVAESAIEGVIS 418 +L +P + A +A+ G I+ Sbjct: 442 -KGGRTHLMSPLMAAAAALAGEIT 464 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: 507 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 428 Length of database: 469 Length adjustment: 33 Effective length of query: 395 Effective length of database: 436 Effective search space: 172220 Effective search space used: 172220 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: 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