Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_011842390.1 RSPH17029_RS17535 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000015985.1:WP_011842390.1 Length = 442 Score = 191 bits (484), Expect = 5e-53 Identities = 144/418 (34%), Positives = 202/418 (48%), Gaps = 58/418 (13%) Query: 15 VFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKL-WHTSNLFRVAG 73 V GEG Y+ +GRR+LD + G AV+ LGH+N + AL Q +L + + F Sbjct: 16 VAAEGEGCYILDAEGRRYLDGSGGAAVSCLGHSNAAVRAALHDQLDRLAFAHTGFFTSEP 75 Query: 74 QESLAKRLTEAT--FADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAFHG 131 E LA RL A + V+ + G+EA E KL R+Y E G R R+I Q++HG Sbjct: 76 AERLADRLAAAAPEGIERVYLVSGGSEAVEAALKLARQYFMEVGQPGRHRVIARRQSYHG 135 Query: 132 RTLAAVSAAQQEKLIKGFGPLL---------------------DGFDLVPFGDLEAVRNA 170 TL A++A E F PLL + + L +LEA Sbjct: 136 NTLGALAAGGNEWRRAQFAPLLVETSHVSPCYEYRGRAEDESLEAYGLRVADELEAEIQR 195 Query: 171 VTDETA-GICLEPIQGEGGIRAGSVE----FLRGLREICDEHGLLLFLDEIQCGMGRTGK 225 + ET EP+ G AG+V +L+ +REICD HG+LL LDE+ CGMGRTG Sbjct: 196 LGPETVMAFVAEPVVGA---TAGAVPAVPGYLKRIREICDRHGVLLILDEVMCGMGRTGH 252 Query: 226 LFAHEWAGITPDVMAVAKGIGGGF-PLGACLATEKAASGMTAGT----HGSTYGGNPLAT 280 LFA G+ PD++ +AKG+G G+ P+GA L + + AG+ HG TY G+ +A Sbjct: 253 LFACAEDGVAPDMITIAKGLGAGYQPIGALLVQGRLYDAIAAGSGFFQHGHTYMGHAMAA 312 Query: 281 AVGNAVLDKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLAC----- 335 A NAVLD++ L V+R G L+ L + ++P V +RG+GL G+ Sbjct: 313 AAANAVLDEIEGRDLLQAVRRQGARLEGLLQERLGQHPHV-GDIRGRGLFRGIELVADRE 371 Query: 336 -----GPA---VGDVVVALRANGLLSVPAGDNV-------VRLLPPLNIGEAEVEEAV 378 PA + A GL+ P G + + L PP I AE+EE V Sbjct: 372 TKEPFDPARKLHARIKAEAFAGGLICYPMGGTLDGVRGDHILLAPPFIISNAELEELV 429 Lambda K H 0.321 0.139 0.414 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: 486 Number of extensions: 31 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: 389 Length of database: 442 Length adjustment: 31 Effective length of query: 358 Effective length of database: 411 Effective search space: 147138 Effective search space used: 147138 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: 50 (23.9 bits)
This GapMind analysis is from Apr 16 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