Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_013835162.1 THICY_RS03115 diaminobutyrate--2-oxoglutarate transaminase
Query= curated2:Q8ZV07 (383 letters) >NCBI__GCF_000214825.1:WP_013835162.1 Length = 428 Score = 182 bits (463), Expect = 1e-50 Identities = 122/382 (31%), Positives = 206/382 (53%), Gaps = 27/382 (7%) Query: 25 DDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAV-PLNFATPARERFIEEF-SK 82 D +G+RYID G + GH +P I +A+ ++ L+ AT A+ FI F S Sbjct: 34 DVEGKRYIDFFGGAGSLNYGHNHPLINQALITYIQRNGITNALDKATVAKHDFISAFQSI 93 Query: 83 LLPPK---FGVVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFTNSFHGRTMGSLSITWNEK 139 +L P+ + + F+ TG VE A+K+A+K+ ++ ++AFTN++HG ++G+L++T NE Sbjct: 94 ILKPRKMDYKIQFVGPTGANGVETALKLARKMKKRSNVIAFTNAYHGHSLGALAVTGNEF 153 Query: 140 YKKAFEPLYPHVRFGKFN--VPHEVDKL------IGEDT------CCVVVEPIQGEGGVN 185 Y + + +V ++ H++D + +G+ + V+VE IQGEGG+N Sbjct: 154 YHGDYYDVPRNVNKMPYDNYFDHDMDSVDMLRHYLGDGSSGYELPAAVIVESIQGEGGIN 213 Query: 186 PATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGKPVAGGLP 245 A+ +L+ L + LLI DE+Q G GRTG ++F++ G+ PDI T K + G+P Sbjct: 214 VASVGWLQKLSALCKEMDILLIMDEIQVGNGRTGDYFSFERAGIMPDIITLSKSIGTGMP 273 Query: 246 IGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREEDVPGRAERIGAELAKAL 305 + + + + DV+ PGEH TF GN+ A AAA L R +D G ++ A Sbjct: 274 MSIVLMKPSV-DVWSPGEHTGTFRGNSYAFIAGAAALELWRNDDFSRSIRAKGKQVEAAF 332 Query: 306 GDTGSRL---AVRVKGMGLMLGLELRVK--ADQFIQPLLERGVMALTAGVN--TLRFLPP 358 D +R V+G+G++ GLE V+ ++ + +RG+M TAG + L+FL P Sbjct: 333 KDFQARFPGWITDVRGLGMIWGLESLVEGFCNEVSKQAFQRGLMMETAGASDQVLKFLGP 392 Query: 359 YMISKEDVEVVHAAVTEVLKKA 380 +IS+ ++ +T+ + A Sbjct: 393 LVISETELNEGFEILTDAILAA 414 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: 346 Number of extensions: 17 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: 428 Length adjustment: 31 Effective length of query: 352 Effective length of database: 397 Effective search space: 139744 Effective search space used: 139744 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