Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_027721528.1 H589_RS0107920 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_000425265.1:WP_027721528.1 Length = 386 Score = 251 bits (641), Expect = 2e-71 Identities = 146/388 (37%), Positives = 222/388 (57%), Gaps = 16/388 (4%) Query: 5 LASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTK 64 ++ R + P + + KA+++ +G +I GEPDFDTPD IK+AC A+ +G+T Sbjct: 4 ISKRACEITPFLVMDVLEKAQQMEREGRSIIHMEIGEPDFDTPDCIKKACCEAMDKGETH 63 Query: 65 YAPSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSP 124 Y S GIPELREAI++ V+ P ++++ G + L+F ILD+GD V++ P Sbjct: 64 YTHSLGIPELREAISKYHKDRYNVDVDPDRVIITQGTSPAMLLLFTFILDKGDNVIVSDP 123 Query: 125 YWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEE 184 + Y I F G + +E GFQ E +K+ + +TKAI+INSP+NPTG + Sbjct: 124 CYACYSNFISFAGAEANRITTFEEDGFQYRPEAIKKAINTKTKAILINSPSNPTGTLLSP 183 Query: 185 EELKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMT 244 E +K+IA G +IISDE Y VYG+ K S ++D F +N FSK ++MT Sbjct: 184 ERMKEIAGM----GPWIISDEIYHGLVYGE-KEHSILEYTDH----AFVLNGFSKLFAMT 234 Query: 245 GWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRR 304 GWR+GY+ PE+Y + + L + + AQ + AL +S D VN ++N ++ RR Sbjct: 235 GWRLGYIISPEKYVRPLQKLCQNFFISANSMAQRAGVAAL--TESWDDVNRIKNTYDERR 292 Query: 305 DTAVEELSKIPGMDV-VKPEGAFYIFPDFSAYAEKL-GGDVKLSEFLLEKAKVAVVPGSA 362 ++ L ++ G D+ V+P GAFY+ + A K G +KL+ +LE+A + V PG Sbjct: 293 KYMLKRLREM-GFDIKVEPTGAFYVLVNMKHLAAKFDGSSLKLAFDILEQAGIGVTPGID 351 Query: 363 F--GAPGFLRLSYALSEERLVEGIRRIK 388 F GA G++RLSYA S E L EG+ R++ Sbjct: 352 FGDGAEGYIRLSYANSIENLAEGMDRLE 379 Lambda K H 0.317 0.135 0.383 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: 398 Number of extensions: 18 Number of successful extensions: 6 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: 394 Length of database: 386 Length adjustment: 31 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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 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