Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_086510842.1 BZY95_RS15720 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_002151265.1:WP_086510842.1 Length = 410 Score = 151 bits (381), Expect = 4e-41 Identities = 121/390 (31%), Positives = 185/390 (47%), Gaps = 38/390 (9%) Query: 23 ALELRRQGVDLVALTAGEP---DFDTPEHVKEAARRAL--AQGKTKYAPPAGIPELREAL 77 A L +G ++ L G P F+ PE + + R L AQG Y G+ R+A+ Sbjct: 28 AKRLEDEGHRILKLNIGNPAPFGFEAPEEILQDVMRNLPTAQG---YCDSKGLYSARKAI 84 Query: 78 AEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGG 137 ++ +R+ V E+ + G + + QA+L+ GDEV++ +P + + +GG Sbjct: 85 MQECQRKEIPGVGIEDIFIGNGVSELIVMALQALLNDGDEVLIPAPDYPLWTAAAHLSGG 144 Query: 138 VVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHD 197 V + + PD VR +T T+A+V+ +PNNPTGAVYP EV+ L +A EHD Sbjct: 145 HAVHYRCDEQADWAPDIADVRAKVTSHTRAIVIINPNNPTGAVYPPEVVRELLAIAREHD 204 Query: 198 FYLVSDEIYEHLLYEG-EHFSPGRVAPEHTL--TVNGAAKAFAMTGWRIGYACGPKEVIK 254 + SDEIY+ +LY+G EH S G +A E L T+NG +K++ G+R G+ V Sbjct: 205 LVVFSDEIYDKILYDGTEHVSTGALADEDQLVVTLNGLSKSYRCAGFRSGWMILSGSVAM 264 Query: 255 AMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEG-------- 306 A Q + A++ N A A ++ A Y+ DL+L G Sbjct: 265 QRAQDYIQG------LNMLASMRLCANVPAQHA-IQTALGGYQSINDLILPGGRLLAQRD 317 Query: 307 -----LTAL-GLKAVRPSGAFYVL--MDTS--PIAPDEVRAAERLLEAGVAVVPGTDF-- 354 L A+ G+ + GA Y +D PI D+ + LL+ + +V GT F Sbjct: 318 ITYEKLNAIPGVSCTKAKGALYAFPRLDPKVYPIQDDQKLVLDLLLQEKILLVQGTAFNW 377 Query: 355 AAFGHVRLSYATSEENLRKALERFARVLGR 384 HVR+ + L AL+RFAR L R Sbjct: 378 PEPDHVRIVTLPWADQLGDALDRFARFLAR 407 Lambda K H 0.317 0.133 0.379 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: 367 Number of extensions: 23 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: 385 Length of database: 410 Length adjustment: 31 Effective length of query: 354 Effective length of database: 379 Effective search space: 134166 Effective search space used: 134166 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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