Align acetylornithine transaminase (EC 2.6.1.11) (characterized)
to candidate WP_012536841.1 AFE_RS08900 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::A8J933 (460 letters) >NCBI__GCF_000021485.1:WP_012536841.1 Length = 449 Score = 165 bits (418), Expect = 2e-45 Identities = 144/435 (33%), Positives = 206/435 (47%), Gaps = 58/435 (13%) Query: 66 LQTYGRA-PVVISHGKGAKMWDVEGKEYIDMAAGIAVNALGHSDSQWYAALVEQAEKLAH 124 +Q YG P +I +G ++D +G +D A + N GH + AAL+ Q K+AH Sbjct: 22 MQCYGDDDPWIIDRAEGNYVYDTQGHRCLDAIASLWCNVHGHRHPRLDAALIGQLGKVAH 81 Query: 125 TSNL-YHTQPQVELAKRLVENS--FADKAFFCNTGTEANEGAIKFARK-WARVRAGIDPY 180 ++ L P + LAK LVE + FF G EA E AIK A + W + Sbjct: 82 STALGAGNAPAIRLAKALVEITPPSLQHCFFSEDGAEAVEVAIKMAAQYWCNL------- 134 Query: 181 DGGAVAPYELVSFTSCFHGRTMGALAL----TYKEQYKTPFYPMM--PGHQLAEYNNLES 234 G ++ + +HG T+GA+++ + E Y +P + P + ++ + E Sbjct: 135 --GRPEKRLFLTLDNAYHGDTVGAVSVGGFPLFHEVYGHLLFPTLRLPSPYVLQWEDCEG 192 Query: 235 ----AAAVI----------KKGKTAAVFVEP-VQGEGGVTPSTQAFLKGLRQLCDEAGAL 279 A AV + G+ AAV +E VQG G+ P L G + LC L Sbjct: 193 DPEQATAVWLAVLETTLQKQSGEIAAVILEGGVQGAAGILPFPPGILAGAQHLCRAYEVL 252 Query: 280 LVFDEVQCGLGRTGKLWGHQLFGVEPDMMTLAKPLAGG-LPIGTVLLKQHV-ADVMKP-G 336 L+ DEV G GR+GKL+ + VEPD++ L K L+GG LP+ L +HV A + P G Sbjct: 253 LIIDEVATGFGRSGKLFSCEWESVEPDLLALGKGLSGGYLPVAATLAAEHVYAAFLAPFG 312 Query: 337 D-----HGSTFAGNPLVCHVACSVFDIINSPAFLAAVEAKGERLRAGLRRTMAGNPHVQE 391 + +G T+ NPL C VA + LAA+ K RLRAGL+R G E Sbjct: 313 ETRQFYYGHTYTANPLACAVALENLALFAEGGVLAALPEKIARLRAGLQR-FHGQSWAGE 371 Query: 392 VRGVGLLVGVQL------------DMMAGPVVDAARDMGVMAITAGKGDVIRLVPPLVVT 439 VR GL+ + L D + V AR+MGV + GD++ +VPPL VT Sbjct: 372 VRQFGLMAAIALRDPGTNAPYPYGDRVEYAVCRRAREMGV--YSRPLGDLLTIVPPLSVT 429 Query: 440 DAEIDTACEVLAAAL 454 AEIDT VL A+ Sbjct: 430 AAEIDTILNVLYDAM 444 Lambda K H 0.319 0.134 0.396 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: 538 Number of extensions: 30 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: 460 Length of database: 449 Length adjustment: 33 Effective length of query: 427 Effective length of database: 416 Effective search space: 177632 Effective search space used: 177632 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: 51 (24.3 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