Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 170 bits (430), Expect = 8e-47 Identities = 126/385 (32%), Positives = 182/385 (47%), Gaps = 36/385 (9%) Query: 31 GKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAPHGPYLALMEQLSQFVP 89 G+RY+DF GI V LGH +P +AI QA L H + +P G LA + V Sbjct: 30 GERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHVSNLYGSPQGEALA-----QRIVD 84 Query: 90 VSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTLATLNLNGKV 143 S+ TNSG EA E A+K AR G + +I F FHGR++ ++ + Sbjct: 85 NSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITFKNAFHGRSIGAISATDQP 144 Query: 144 APYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGEG 203 LPG Y +K D ++ ++ A F+ E VQGEG Sbjct: 145 KMRDGFEPLLPGFDY----------------VKFNDLEGAIAKIDDETAGFLVETVQGEG 188 Query: 204 GFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIAG 263 G A F Q LR+ CDE G+L+I+DEIQ G+GRTG+ +A+ GI PD+L AK I Sbjct: 189 GMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKGIGN 248 Query: 264 GMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQAIV 323 G PLGA + +E + G G TY GNP++ AA A L M + E+ + + Sbjct: 249 GFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEKMGERLR 308 Query: 324 SRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLMPSGK 383 + +E+ + G G M GI+ PA ++ V GLL + +G+ Sbjct: 309 AGFEQ-LIPNHDHLFDEIRGKGLMLGIKLK----EPAVSR-DFVAHLRENHGLLTVAAGE 362 Query: 384 ARHIIRLLAPLTIEAEVLEEGLDIL 408 ++ R+L PL IE + E ++ L Sbjct: 363 --NVFRVLPPLVIEESHIAECIEKL 385 Lambda K H 0.320 0.137 0.402 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: 438 Number of extensions: 24 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: 416 Length of database: 398 Length adjustment: 31 Effective length of query: 385 Effective length of database: 367 Effective search space: 141295 Effective search space used: 141295 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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