Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_012506055.1 PAES_RS07515 aminotransferase
Query= curated2:O33822 (383 letters) >NCBI__GCF_000020625.1:WP_012506055.1 Length = 388 Score = 187 bits (475), Expect = 4e-52 Identities = 136/392 (34%), Positives = 206/392 (52%), Gaps = 32/392 (8%) Query: 3 GLSQRVKSMKPSATVAVNARALELRRKGVDLVALTAGEPDFDTPEHVKEAGRRALAQGKT 62 G S+R +S+ S + ++E R G + L+ G D P V E AL+Q + Sbjct: 4 GTSERCRSVLQSD---IRMMSVECHRLGG--INLSQGVCDTPVPGVVLEGASHALSQRQN 58 Query: 63 KYAPPAGIPELREAVAEKFRRENGLEVTPE-ETIVTVGGKQALFNLFQAILDPGDEVIVL 121 Y AGI LREA+AEK+R G++V P+ E +V+ G A++ FQA+L+PGDEVIV Sbjct: 59 SYTHYAGIGGLREALAEKYRTMYGIDVDPQQEIVVSAGATGAMYCAFQALLNPGDEVIVF 118 Query: 122 APYWVSYPEMVRFAGGVPVEVP-TLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGVV 180 PY+ + + VPV + T P+ F + A++ RT+A+++N+P NP+G V Sbjct: 119 EPYYGYHISTLNALQAVPVFLSLTSPDWTF--SEADLEAAVSSRTRAILINTPGNPSGKV 176 Query: 181 YPEEVLRALAEMALQHDFYLVSDEIYEHLIYEG-AHFSPGTL--APEHTITVNGAAKAFA 237 + L+ +A+ A +HD ++ +DEIYEH +Y+G H SP L + T+ ++G +K F+ Sbjct: 177 FTLAELQRIADFAEEHDLFVFTDEIYEHFLYDGRRHHSPFALPGMRKRTVLISGFSKTFS 236 Query: 238 MTGWRIGYACGPKAVIKA------MADVSSQSTTSPDTIAQWATLEALTNREASMAFIAM 291 +TGWRIGYA +A + V + S P A ATL+ + ++++ Sbjct: 237 VTGWRIGYAISDARWAQAIGYFNDLVYVCAPSALQPGVAAGLATLD-------TSYYLSL 289 Query: 292 AREAYRKRRDLLLEGLSRIGLEAVRPSGAFYVLMDTS--PFAPNEVEAAERLLMAGVAVV 349 + E Y +R+ L GL AV P GA+YVL D S P + +A L GVA V Sbjct: 290 SAE-YGFKRNRFCRALGEAGLNAVLPQGAYYVLADVSHLPGSTTRDKAMHILRTTGVASV 348 Query: 350 PGTEFAAFGH----VRLSYATGEENLKKALER 377 PG+ F + VR YA + L A ER Sbjct: 349 PGSAFFRNENDQHLVRFCYAKDDVVLDAACER 380 Lambda K H 0.317 0.133 0.382 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: 359 Number of extensions: 23 Number of successful extensions: 5 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: 383 Length of database: 388 Length adjustment: 30 Effective length of query: 353 Effective length of database: 358 Effective search space: 126374 Effective search space used: 126374 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