Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78 (characterized)
to candidate WP_041702288.1 PAES_RS06865 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q8KDS8 (400 letters) >NCBI__GCF_000020625.1:WP_041702288.1 Length = 402 Score = 607 bits (1564), Expect = e-178 Identities = 299/393 (76%), Positives = 338/393 (86%) Query: 7 ERFLSRRVLSMQESQTMKITGLAKKMQAEGKDVVSLSAGEPDFPTPENVCEAGIEAIRKG 66 E++L+RRVL+MQESQTM+ITGLAKKM+AEGKD+VSLSAGEPDFPTP V +AGIEAI G Sbjct: 9 EKYLTRRVLNMQESQTMRITGLAKKMKAEGKDIVSLSAGEPDFPTPLFVSQAGIEAIDSG 68 Query: 67 FTRYTANSGIPELKKAIIRKLQRDNGLEYAEDEIIVSNGGKQALANTFLALCDEGDEVIV 126 FTRYTANSGI ELK A+I KL+RDN L+Y DE+IVSNGGKQ L N LALC EGDEVI+ Sbjct: 69 FTRYTANSGIAELKSAVIAKLKRDNQLDYTPDEVIVSNGGKQTLINAILALCQEGDEVII 128 Query: 127 PAPYWVSFPEMARLAEATPVIVETSIETGYKMTPEQLAAAITPKTRILVLNSPSNPSGAV 186 PAPYWVSFPEM RLA A+PV V TSIE GYKMTPE L AIT KT++ +LNSPSNPSGAV Sbjct: 129 PAPYWVSFPEMVRLAGASPVTVPTSIENGYKMTPEDLENAITDKTKLFILNSPSNPSGAV 188 Query: 187 YNEAEVRALMQVIEGKEIFVLSDEMYDMICYGGVRPFSPARIPEMKPWVIVSNGTSKSYS 246 YNE EV ALMQV+EG+ IFV+SDEMYD I YG V+P+SPARI M+ WV+VSNG SK+Y+ Sbjct: 189 YNEQEVTALMQVLEGRGIFVISDEMYDKIVYGDVKPYSPARIEAMRDWVLVSNGVSKTYA 248 Query: 247 MTGWRIGYLAAPKWIINACDKIQSQTTSNANSIAQKAAVAALDGDQSIVEQRRAEFEKRR 306 MTGWRIGYLA PKWII ACDKIQSQTTSN NSIAQKAA AAL+GDQ +VE RR EFEKRR Sbjct: 249 MTGWRIGYLAGPKWIIKACDKIQSQTTSNPNSIAQKAAAAALNGDQQVVEDRRLEFEKRR 308 Query: 307 DFMFRELNTISGIECTLPEGAFYIFPSIKGLLGKTFGGKVMKDSTDVAEYLLTEHYVATV 366 D+M++ LN I GI +LPEGAFYIFPS+KG+LGKTF G+ + +S+DVAEYLL +HYVATV Sbjct: 309 DYMYKALNEIPGITASLPEGAFYIFPSVKGVLGKTFNGRYLANSSDVAEYLLLDHYVATV 368 Query: 367 PGDAFGAPENLRLSYAASIEELAEAVNRIRKAF 399 PGDAFGAPENLRLSYAASI EL EAV RIRKAF Sbjct: 369 PGDAFGAPENLRLSYAASISELEEAVRRIRKAF 401 Lambda K H 0.316 0.132 0.376 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: 581 Number of extensions: 10 Number of successful extensions: 1 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: 400 Length of database: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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 (21.6 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