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 WP_012278671.1 SHAL_RS18655 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000019185.1:WP_012278671.1 Length = 405 Score = 218 bits (555), Expect = 3e-61 Identities = 137/392 (34%), Positives = 205/392 (52%), Gaps = 34/392 (8%) Query: 29 RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88 R E RVWD EG+EY+DFAGGIAV GH HP +V A++ Q +KL H V+ EP LE Sbjct: 29 RGEGSRVWDQEGKEYIDFAGGIAVNCLGHCHPALVGALKTQGEKLWHLS-NVMTNEPALE 87 Query: 89 LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATKRSGTIAFSGAYHGRT 142 L + V FA++ +G+EA E A+K+ R ++ IAF A+HGRT Sbjct: 88 LA---TKLVEATFAERVYFANSGAEANEAALKLVRRYAMDKFGAEKDQIIAFDKAFHGRT 144 Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAA 202 +T+++ G+ YS G G P +++ P + I +A+ S + A Sbjct: 145 FFTVSVGGQA-AYSDGFGPKP----QSITHVPFNDIEALEAVFS-----------DKTCA 188 Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262 +++EP+QGEGG + P F++ +RALCD+H +L+ DEVQ+G GR G L+A + V PD Sbjct: 189 VMMEPLQGEGGIIDADPEFLKAVRALCDKHNALLVFDEVQTGVGRLGELYAYMRGDVVPD 248 Query: 263 LTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQ 322 + T AK++ GGFP+A + E+ + G G TY GNP+AC V+ V +L Sbjct: 249 VLTTAKALGGGFPIAAMLTTKEIAAHLKIGTHGSTYGGNPLACAVGNAVMDVVNTPEVLN 308 Query: 323 KANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARD 382 Q +DGL I +K+ ++RG G +I + N E + + Sbjct: 309 GVKHREQLFRDGLNKINDKYDVFSEIRGQGLLIGAVV------NSKYQGRAKEFLVAGIN 362 Query: 383 KGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414 +G++ L G NV+R L I + I +GL Sbjct: 363 EGVMSLVAGA--NVVRFTPSLVIPETDIAEGL 392 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: 435 Number of extensions: 16 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: 426 Length of database: 405 Length adjustment: 31 Effective length of query: 395 Effective length of database: 374 Effective search space: 147730 Effective search space used: 147730 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 24 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