Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_029911017.1 P166_RS0108225 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q8ZV07 (383 letters) >NCBI__GCF_000711315.1:WP_029911017.1 Length = 422 Score = 189 bits (479), Expect = 2e-52 Identities = 136/412 (33%), Positives = 213/412 (51%), Gaps = 48/412 (11%) Query: 7 YYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIW-AVP 65 Y R + K M +WDD G+RY+D G + GH NP I +AV K ++E Sbjct: 19 YIRSFPTLFSKSKMAEIWDDDGKRYVDFFAGAGALNYGHNNPVINDAVIKYLQEDGIGHA 78 Query: 66 LNFATPARERFIEEF-SKLLPPK---FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFT 121 L+ AT A+ FIE F + +L P+ + + F+ TGT A+E A+KIA+KV + +++FT Sbjct: 79 LDMATVAKRDFIESFVNNILKPRNLDYKIQFVGPTGTNAIETALKIARKVKGRKQVMSFT 138 Query: 122 NSFHGRTMGSLSITWNEKYKKAFEPLYPHVRFGKFN--VPHEVDKL-----IGEDT---- 170 N FHG +MGSLSIT N Y + + F+ + +VD + I ED Sbjct: 139 NGFHGMSMGSLSITGNSYYHDESYGVPGYTTQVPFHNYLGDKVDTIAYLHKILEDASSGT 198 Query: 171 ---CCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKY 227 +V+E IQ EGG+N A +LK+LRE + LLI D++Q G GR+ ++F++ Sbjct: 199 ELPAAIVLETIQAEGGINVAGAPWLKSLREICDKFDILLIVDDIQAGNGRSSDFFSFERA 258 Query: 228 GVEPDIFTAGKPVAGGLPIGLAVAREDFGDVFEPGEHGSTFAG-NAVVMAAAAAASRLLR 286 G+ PDI T K V GG P+ + + + + D + PGEH TF G N +AA AA + Sbjct: 259 GIVPDIVTLSKSVGGGHPMSIVLMKPEL-DKWSPGEHSGTFRGFNLAFVAAKAAIDKYWS 317 Query: 287 EED-----------VPGRAERIGAELAKALGDTGSRLAVRVKGMGLMLGLELR--VKADQ 333 +D V R +++ + KA+ + ++G G++ G E R A + Sbjct: 318 NKDFQAEIKQKSEWVQQRMQQLALKFPKAIRE--------IRGHGMIWGAEFRDPEVASK 369 Query: 334 FIQPLLERGVMALTAGV--NTLRFLPPYMISKEDV----EVVHAAVTEVLKK 379 + G++ TAG ++FL P +I+KE + +++ +A T+VL K Sbjct: 370 VCEASFHEGLVVETAGAEGEVIKFLGPLIITKELIDEGFDILESATTKVLAK 421 Lambda K H 0.320 0.138 0.408 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: 354 Number of extensions: 19 Number of successful extensions: 4 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: 422 Length adjustment: 31 Effective length of query: 352 Effective length of database: 391 Effective search space: 137632 Effective search space used: 137632 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