Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; EC 3.7.1.9; 2-hydroxymuconic semialdehyde hydrolase (uncharacterized)
to candidate BPHYT_RS23610 BPHYT_RS23610 alpha/beta hydrolase
Query= curated2:P19076 (283 letters) >FitnessBrowser__BFirm:BPHYT_RS23610 Length = 331 Score = 89.0 bits (219), Expect = 1e-22 Identities = 91/288 (31%), Positives = 133/288 (46%), Gaps = 29/288 (10%) Query: 4 PQNSPEIGREIIAAGIRTNL--HDSGAGFPLMMIHGSGPGVTAWANWRLVMPELAKSRRV 61 P + P I RE IA + ++ G G P+++ G + W + +LAK V Sbjct: 48 PDHKPWI-REQIAHTVNGDIAYFRFGHGTPIVLQTGFRATLAEWD--AAFLTDLAKRHEV 104 Query: 62 IAPDMLGFGYSERPADAQYNRDVWVDHAVGVLDALEIEQADLVGNSFGGGIALALAIRHP 121 I D G G SE A + RD+ +D A ++D L + VG S GG IA LA+ P Sbjct: 105 IVFDNRGIGRSEPAASSFTARDMTLD-AAALIDTLRLSDVTFVGWSMGGAIAQQLALDAP 163 Query: 122 ERVRRLVLM-----GSAGVSFPITEGLDAVWGYNP--SFAEMRRLLDIFAFDRNLVNDEL 174 VRR+VLM GS GV P+T ++A N +F ++ R+L F N V+ Sbjct: 164 LAVRRIVLMSAPAPGSLGV--PVTPDVEATLSGNAGTTFMDVMRVL----FPPNAVDAAQ 217 Query: 175 AELRYQ----ASIRPGFHESFAAMFPAPRQRWVDGLASAEAAIRALPH---ETLVIHGRE 227 R AS RP + +A + + +S EAA AL + TL++ G + Sbjct: 218 RCFRQNMFQPASYRP---PAISATVTEGQSVLLHDWSSDEAAAAALKNVRLATLILTGAD 274 Query: 228 DQIIPLQTSLTLADWIARAQLHVFGQCGHWTQIEHAARFASLVGDFLA 275 DQ++P Q S LA I AQL V GH ++ A+ + F+A Sbjct: 275 DQVLPKQNSEALAGQIPHAQLLVVRSAGHAMMYQYPHALAAAINTFIA 322 Lambda K H 0.323 0.137 0.424 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: 224 Number of extensions: 13 Number of successful extensions: 3 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: 283 Length of database: 331 Length adjustment: 27 Effective length of query: 256 Effective length of database: 304 Effective search space: 77824 Effective search space used: 77824 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 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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