Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_012384241.1 BIND_RS06310 aspartate aminotransferase family protein
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_000019845.1:WP_012384241.1 Length = 444 Score = 275 bits (702), Expect = 3e-78 Identities = 159/434 (36%), Positives = 241/434 (55%), Gaps = 12/434 (2%) Query: 17 EHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAA 76 E + PF+ + K K PRI+ +AK ++ + ++G ILDG AGLWC G+ RD++ A Sbjct: 14 EAYWMPFTANRAFK-KSPRIVASAKDMHYYTADGKPILDGTAGLWCCNAGHSRDKIVQAI 72 Query: 77 SKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136 Q EL + F Q HP V LA I+ +AP ++HVFF SGSE DT L++ Y Sbjct: 73 QAQAAELDFAPPF-QFGHPKVFALAARIAALAPGDLDHVFFGNSGSEAVDTALKIALAYH 131 Query: 137 AIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDM 196 I+GQ ++ +I R YHG G ++GG+ + + G+ H+P Y E Sbjct: 132 NIQGQGSRVRLIGRERAYHGVGFGGGAVGGIPGNRKAFGALLAGVDHLPTTYNRAEQAFT 191 Query: 197 TPE-EFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDI 255 E E+G A++LE+ + T+ A I EP+ G+ GV+ PP Y +++ I KY I Sbjct: 192 KGEPEWGGHLADELEKLVALHDASTIAAVIVEPMSGSTGVLPPPKGYLQKLRAICDKYGI 251 Query: 256 LFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG 315 L + DEVICG+GR G F ++ YG+ PDM+T AKG+TSG +PMGG+++R + E +G Sbjct: 252 LLIFDEVICGYGRLGYAFAAERYGVVPDMITFAKGITSGTVPMGGVLIRKPIYEAFMKGP 311 Query: 316 ----DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVG 371 + HG+TYSGHP+A A L + + +EE + E R + P + L P + Sbjct: 312 ELAVELTHGYTYSGHPLACAAGLATLDLYKEEGLFERAR-KLEPVWADAVHGLKSLPNIL 370 Query: 372 EVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITK 431 ++R VGL AI+L A A GK + + + L+ R GD++I+ PPL+I++ Sbjct: 371 DIRTVGLTAAIDL----APIADAPGKRAFGVMDKAFHELDLLTRIAGDSIILTPPLIISE 426 Query: 432 AEIDELVTKARKCL 445 +I E+V K K + Sbjct: 427 GQIGEIVEKTGKAI 440 Lambda K H 0.320 0.140 0.428 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: 568 Number of extensions: 31 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: 454 Length of database: 444 Length adjustment: 33 Effective length of query: 421 Effective length of database: 411 Effective search space: 173031 Effective search space used: 173031 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 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