Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate YP_004145044.1 Mesci_5987 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000185905.1:YP_004145044.1 Length = 399 Score = 246 bits (629), Expect = 6e-70 Identities = 152/372 (40%), Positives = 205/372 (55%), Gaps = 23/372 (6%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R L GEG ++ +KG RYLD GI VN LGH+HP V ++ Q K+ ++E Sbjct: 12 RAPLAFDHGEGTWLITDKGERYLDFAGGIAVNSLGHSHPHLVAALTEQAAKLWHVSNLYE 71 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATGRSE---IVAMTNAFH 118 + + E L+ + V+ NSG EA+E AIK AR G E I+ AFH Sbjct: 72 IPGQSRLGERLADATFADKVFFTNSGAEALECAIKTARRYHFVKGHPERFRIITFEGAFH 131 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GRTL +++A + KY EGFGP V GF + F++++AA++AIT ETAA++ EP+QGEGGI Sbjct: 132 GRTLATIAAGGQYKYLEGFGPKVEGFDQVGFDDIDAAEKAITPETAAILIEPVQGEGGIR 191 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237 P + +K LR L E G LLI DEVQ G+ RTGK A E GV PDI+ + KGIG GFP Sbjct: 192 PVPTQSLKRLRQLCEQHGLLLIYDEVQCGIGRTGKLFAHEWSGVTPDIMAIAKGIGGGFP 251 Query: 238 VSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFM------ 287 + L E + G HG+TFGGNPLA L ++ D +E K + Sbjct: 252 MGACLATDEAAVGMTAGVHGTTFGGNPLAMAVGNAVLDVVLEDGFLEDVQRKALLMKQGL 311 Query: 288 -----EFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLII 342 EF E + RG GLM+G+ P AL+++ +L AG+ VIRLLPPL + Sbjct: 312 ASVADEFP-EIIEDIRGAGLMLGLKCAMPNTKVNMALRDQHLLAVPAGDNVIRLLPPLTV 370 Query: 343 EGDTLEEARKEI 354 + +A I Sbjct: 371 TDAEIHDALNRI 382 Lambda K H 0.320 0.140 0.410 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: 388 Number of extensions: 19 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: 362 Length of database: 399 Length adjustment: 30 Effective length of query: 332 Effective length of database: 369 Effective search space: 122508 Effective search space used: 122508 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 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