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 Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__SynE:Synpcc7942_0645 Length = 453 Score = 159 bits (403), Expect = 1e-43 Identities = 112/352 (31%), Positives = 169/352 (48%), Gaps = 17/352 (4%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV-LA 82 PI DR ++ WDV+G Y+D+ G GH HP+V+ A++ ++K T F A Sbjct: 61 PIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEK--GTSFGAPCA 118 Query: 83 YEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRT 142 E L E++ VP + V +G+EA +++ RA T R I F G YHG Sbjct: 119 LENV--LAEMVIDAVPS--IEMVRFVNSGTEACMAVLRLMRAYTGRDKIIKFEGCYHGHA 174 Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAA 202 L G + G+ PG V ++ L D + ++ +F + P +IA Sbjct: 175 DMFLVKAGS-GVATLGLPDSPG-VPKSTTANTLTAPYND--LEAVKALFAEN--PGEIAG 228 Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262 +++EP+ G GF F++ LR + EH +L+ DEV +G R E+ GV PD Sbjct: 229 VILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGF-RIAYGGVQEKFGVTPD 287 Query: 263 LTTFAKSIAGGFPLAGVTGRAEVMDAVAPGG---LGGTYAGNPIACVAALEVLKVFEQEN 319 LTT K I GG P+ G+ E+M VAP G GT +GNP+A A ++ L++ Q Sbjct: 288 LTTLGKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQPG 347 Query: 320 LLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAK 371 + + + ++L DGLLAIA++ + M E HN DAK Sbjct: 348 TYEYLDQITKRLSDGLLAIAQETGHAACGGQVSGMFGFFFTEGPVHNYEDAK 399 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: 501 Number of extensions: 28 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: 453 Length adjustment: 32 Effective length of query: 394 Effective length of database: 421 Effective search space: 165874 Effective search space used: 165874 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: 51 (24.3 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