Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AO353_29000 AO353_29000 pyridoxal-5'-phosphate-dependent protein subunit beta
Query= BRENDA::Q96GA7 (329 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29000 Length = 303 Score = 223 bits (568), Expect = 5e-63 Identities = 133/307 (43%), Positives = 184/307 (59%), Gaps = 14/307 (4%) Query: 15 HVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQEMAKKGCRHLVCSSGGN 74 H+ TPL+ LS ++LK EN+QPSGSFK+RG+G C A++G + +VC SGGN Sbjct: 3 HIRTPLILHPGLS-TPSRRIWLKLENLQPSGSFKLRGMGLLCTRAAEQGMKKVVCPSGGN 61 Query: 75 AGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEGAEVQLTGKVWDEANLRAQELAKRD 134 AG A A AA LG+ A+I++P +T R+ GA+V + G+VWDEAN A ELA Sbjct: 62 AGYATAVAAAALGLEASIIVPHTTPESTRARIAKTGAQVIVHGQVWDEANQLALELANAP 121 Query: 135 GWENVPPFDHPLIWKGHASLVQELKAVLRTPP--GALVLAVGGGGLLAGVVAGLLEVGWQ 192 E VP FDHP +W+GH++++ E +L+ P +V +VGGGGLLAG++ GL Sbjct: 122 DTEYVPAFDHPTLWEGHSTMIDE---ILQDCPQVDTIVASVGGGGLLAGILTGLERHARL 178 Query: 193 HVPIIAMETHGAHCFNAAITAGKLVTLPDITSVAKSLGAKTVAARALECMQVCKIHSEVV 252 IIA ET GA F+AA+ AG V L +I+S+A SLGA VA +E +Q V+ Sbjct: 179 DCRIIACETEGAASFDAAVKAGHPVKLSEISSIASSLGALQVAQWPVEHIQHFPHTCVVL 238 Query: 253 EDTEAVSAVQQLLDDERMLVEPACGAALAAIYSGLLRRLQAEGCLPPSLTSVVVIVCGGN 312 D EA+ V + DD R LVEPACG +LA Y +A VV+IVCGG Sbjct: 239 TDAEAIMGVVRYADDLRQLVEPACGVSLAVAYLDHPAIAEAH--------DVVIIVCGGI 290 Query: 313 NINSREL 319 +I+++++ Sbjct: 291 SISAQKV 297 Lambda K H 0.319 0.134 0.404 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: 208 Number of extensions: 8 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: 329 Length of database: 303 Length adjustment: 27 Effective length of query: 302 Effective length of database: 276 Effective search space: 83352 Effective search space used: 83352 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: 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