Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate WP_025273617.1 HALAL_RS0108625 homogentisate 1,2-dioxygenase
Query= reanno::MR1:201124 (386 letters) >NCBI__GCF_000527155.1:WP_025273617.1 Length = 395 Score = 280 bits (715), Expect = 7e-80 Identities = 154/397 (38%), Positives = 214/397 (53%), Gaps = 22/397 (5%) Query: 1 MPFYVKQGQVPHKRHIAFEKENGELYREELFSTHGFSNIYSNKYHHNMPTKALEVAPYRL 60 MPFY + G++P KRH F + +G LY EEL GFS+ S YH PT Sbjct: 1 MPFYQQVGEIPPKRHTQFRQPDGTLYHEELMGQEGFSSDSSLLYHRYRPTAISSSEVVNP 60 Query: 61 GHGAHWEDSLVQNYKLDSRSADREGN-FFSARNKIFYNNDVAIYTAKVTQDTAEFYRNAY 119 GA + ++ L + + GN R + N D I A T T+ YRN+ Sbjct: 61 DDGAPSPNHPLKPRHLRTHKLNGTGNDAIFGRQPLLSNADCRISYANATV-TSPLYRNSL 119 Query: 120 ADEVVFVHEGEGTLYSEYGTLEIKKWDYLVIPRGTTHQLKFNNYSNVRLFVIEAFSMVEV 179 DE ++V G T+ + +G ++I DYL+IP T +++ +R V+E+ + Sbjct: 120 GDECIYVESGSATVQTSFGEIDISGGDYLIIPMATIYRVIPTGDDPLRTLVVESTGHITP 179 Query: 180 PKHCRNEYGQLLESAPYCERDLRTPI----LQAAVVE-------RGAFPLVCKFGDKYQL 228 PK + GQ LE +PYCERDLR P L+ V+ RG+ L +F Sbjct: 180 PKRYLSVRGQFLEHSPYCERDLRAPTSPLQLEGDNVDVYVQHKGRGSQTLWTRF------ 233 Query: 229 TTLEWHPFDLVGWDGCVYPWAFNITEYAPKVGKIHLPPSDHLVFTAHNFVVCNFVPRPYD 288 T + HPFD+VGWDGC+YPW F+I ++ P G+IH PP H F NFV+C+FVPR D Sbjct: 234 -TYDKHPFDVVGWDGCLYPWVFSIHDFEPITGRIHQPPPVHQTFQGPNFVICSFVPRKVD 292 Query: 289 FHERAIPAPYYHNNIDSDEVLYYVDGDFMSR--TGIEAGYITLHQKGVAHGPQPGRTEAS 346 +H +IP PY H+N+DSDEV++Y GD+ +R +GIE G I++H G HGPQPG E + Sbjct: 293 YHPDSIPVPYNHHNVDSDEVMFYTGGDYEARKGSGIEQGSISVHPSGFTHGPQPGAPERA 352 Query: 347 IGKKETYEYAVMVDTFAPLKLTEHVQHCMSKDYNRSW 383 IG + E AVM+DTF PL+L C Y +W Sbjct: 353 IGAESFDELAVMIDTFRPLELCGAAFDCEDTGYAWTW 389 Lambda K H 0.321 0.137 0.435 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: 505 Number of extensions: 26 Number of successful extensions: 4 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: 386 Length of database: 395 Length adjustment: 31 Effective length of query: 355 Effective length of database: 364 Effective search space: 129220 Effective search space used: 129220 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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:
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