Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Pedo557:CA265_RS15205 Length = 378 Score = 195 bits (496), Expect = 2e-54 Identities = 131/399 (32%), Positives = 202/399 (50%), Gaps = 47/399 (11%) Query: 29 RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88 RA+ ++D + ++++D GI V N GH HP VV A++ Q + H ++ Y Y++ Sbjct: 6 RAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMH----LMVYGEYVQ 61 Query: 89 LCEIMNQKVPGDFAKKTLLVT----TGSEAVENAVKIARAATKRSGTIAFSGAYHGRTHY 144 ++ K D ++L T +G+EAVE A+K+A+ T R G IA AYHG T Sbjct: 62 TPQVNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKGFIACKNAYHGSTQG 121 Query: 145 TLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIV 204 +L + + YS+G G HV E + +A + +I +IAA+ Sbjct: 122 AESLM-ESDFYSSGYGPFLPHV----------SFIEHNNLADLEKI------TNEIAAVF 164 Query: 205 IEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLT 264 IEP+QGE G S ++MQ LR C E G +LI DE+QSG GR+G +FA E V PD+ Sbjct: 165 IEPIQGEAGIRVSDLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVL 224 Query: 265 TFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG---TYAGNPIACVAALEVLKVFEQENLL 321 AK I GG P+ E+M ++ + G T+ G+P+ C A L L+ ++++ Sbjct: 225 LLAKGIGGGMPIGAFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIV 284 Query: 322 QKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARAR 381 + + GQ K L +HP I ++RG G M+A+E FE+ + NK +I+ Sbjct: 285 DEVEEKGQLFKQLL-----QHPAIKEIRGKGLMLAVE-FENFEINK-------KIIDACI 331 Query: 382 DKGLI---LLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 G++ L C N +RI PL I +I + II Sbjct: 332 LDGVLSDWFLHCS---NSMRIAPPLIITKEEIAEACTII 367 Lambda K H 0.320 0.137 0.401 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: 383 Number of extensions: 23 Number of successful extensions: 5 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: 426 Length of database: 378 Length adjustment: 31 Effective length of query: 395 Effective length of database: 347 Effective search space: 137065 Effective search space used: 137065 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