Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013835847.1 THICY_RS06630 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000214825.1:WP_013835847.1 Length = 390 Score = 176 bits (445), Expect = 1e-48 Identities = 126/383 (32%), Positives = 190/383 (49%), Gaps = 35/383 (9%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+T +G A ++D Y+D V GI V +LGH +PA+ +A+ Q+ L H + + Sbjct: 12 PVTFHYGEGALLYDEQDNAYLDAVSGIAVCSLGHAHPAIAQALCEQSKTLIHTS-----N 66 Query: 75 GPYLALMEQLS-QFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAI-----IAFDGG 128 ++A +QL + V +S NSGAEA E A+K+AR + I I + Sbjct: 67 LYHVAKQQQLGDKLVAISGMDKVFFGNSGAEANEAAIKMARKYGHSKGISHAQIIVMENS 126 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRTLATL+ G V+ YP + V D + +V A+ Sbjct: 127 FHGRTLATLSATGSAK------------VHDGFYPLVEGFVRVP-----FDNVEAVANAI 169 Query: 189 ED---VAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245 + V A + EPVQGEGG P + +ALR CDE +L++IDEIQ+G GRTG+ FAF Sbjct: 170 ANNPNVVAILVEPVQGEGGVHVPKPGYLKALRALCDEHDLLLMIDEIQAGIGRTGKWFAF 229 Query: 246 PRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ 305 GI PD+L LAK++ G+P+GA + R + G G T+ GNP++CAA LA + Sbjct: 230 QHEGILPDVLSLAKALGNGVPIGASLARGKAAELFAPGNHGTTFGGNPLACAAGLAVIET 289 Query: 306 MTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLA 365 + N +Q +++ ++ A+ P + + G G M GI+ G LA Sbjct: 290 LEYHNYIDLVAKQGAELLAAFKTALAN--IPGVVDIRGKGYMIGIQLDRPCGDLVKMALA 347 Query: 366 K--VMEAARARGLLLMPSGKARH 386 ++ R + L+P+ H Sbjct: 348 DKLLINVTRGDTVRLLPTFVMTH 370 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: 362 Number of extensions: 21 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: 390 Length adjustment: 31 Effective length of query: 385 Effective length of database: 359 Effective search space: 138215 Effective search space used: 138215 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