Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate BPHYT_RS09280 BPHYT_RS09280 pyridoxal-5'-phosphate-dependent protein subunit beta
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__BFirm:BPHYT_RS09280 Length = 344 Score = 145 bits (365), Expect = 3e-39 Identities = 96/305 (31%), Positives = 153/305 (50%), Gaps = 19/305 (6%) Query: 20 VLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKA 79 V R PV++ L+ V+ K E Q SFK RGA+ + L E Q++ Sbjct: 35 VARTPVFDRVDFPSLE---------GTVVNFKFELLQAGGSFKARGAFTNLLALDEAQRS 85 Query: 80 HGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAK 139 GV S GNHA VA+++ RLGV A +V+ A +V R + E++ F E Sbjct: 86 AGVTCVSGGNHAVAVAYAAMRLGVSAKVVLFRAANPARVALCRQYRAEIV-----FAEDI 140 Query: 140 AKAIELSQ----QQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAG 195 A+A EL + ++G +V PF+ + G TL E Q L+ V +P+GGGGLAAG Sbjct: 141 AEAFELVRRIEAEEGRYFVHPFNGYRTVLGSATLGYEWATQTPDLEAVILPIGGGGLAAG 200 Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255 VA ++ P + V VE E + + + A H V + ++ A+ + ++ LC Sbjct: 201 VATAMRLANPNVHVYGVEPEGADVMGKSFAANHTVKMRQMRGIADSLMSPHTEQYSYELC 260 Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILS 315 + ++D ++TV D + AAM LF ++ EP+ A A AG+ + ++G+R+ +L Sbjct: 261 RRHIDQLVTVSDDQLRAAMLTLFGQLKLAVEPACAAATAGLLGPLR-EQLQGKRVGVLLC 319 Query: 316 GANVN 320 G N + Sbjct: 320 GTNTD 324 Lambda K H 0.321 0.138 0.403 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: 355 Number of extensions: 23 Number of successful extensions: 2 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: 514 Length of database: 344 Length adjustment: 32 Effective length of query: 482 Effective length of database: 312 Effective search space: 150384 Effective search space used: 150384 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 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