Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_068170525.1 HTA01S_RS10520 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_001592305.1:WP_068170525.1 Length = 479 Score = 571 bits (1471), Expect = e-167 Identities = 281/461 (60%), Positives = 348/461 (75%), Gaps = 6/461 (1%) Query: 4 QQQDTISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWC 63 +QQDT A+QA+D+AH+LHPFTD A LA RG RVI RA+ +Y+WD++G K+LDAM+GLWC Sbjct: 17 EQQDT-KAIQALDSAHYLHPFTDHAGLASRGARVITRADNIYVWDSEGAKILDAMSGLWC 75 Query: 64 VNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNR----VFFT 119 VN GYGRK +ADAAY Q+ TLPFYN+FF T+ PA++LA+K+ASLAP R VFF+ Sbjct: 76 VNAGYGRKELADAAYQQMMTLPFYNSFFNTTNVPAVQLATKLASLAPKVGGRSFEHVFFS 135 Query: 120 GSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPI 179 SGSE+NDTN+RMVRRYWDL G P +K IISR NAYHGST+AGASLGGMG MH QGDLPI Sbjct: 136 SSGSESNDTNVRMVRRYWDLLGQPQRKVIISRNNAYHGSTMAGASLGGMGGMHAQGDLPI 195 Query: 180 PGIVHIDQPYWFGEGRDMSPEA-FGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVII 238 P I HI+QPY+F R EA FG + A LEAKILE+G DKVAAFIAEP QGAGGVII Sbjct: 196 PNITHIEQPYFFENARPGESEADFGRRAAGWLEAKILEVGADKVAAFIAEPVQGAGGVII 255 Query: 239 PPDSYWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIP 298 PP++YW EI+RI+++Y IL I DEVI FGR G+WFA + G +PDL+T AKG+TSGYIP Sbjct: 256 PPETYWPEIQRIVDQYGILLISDEVICAFGRLGHWFAYEKFGYRPDLVTFAKGVTSGYIP 315 Query: 299 MGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPY 358 +GGV+V DRVA VLI GGEF HG+TYSGHPVA AVAL N+ ++E E LV +V+ DTGPY Sbjct: 316 LGGVMVGDRVARVLIEKGGEFNHGYTYSGHPVACAVALANLELMERENLVGRVKDDTGPY 375 Query: 359 LQDRLQTLSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMR 418 L R L HPLVG G V + LV +K + F +++ GM+CR C ++GL+MR Sbjct: 376 LARRFAELKDHPLVGGAETCGFVAGLVLVKNKATNAMFDADLGVGMICRGHCFKNGLIMR 435 Query: 419 AVGDTMIISPPLCITRDEIDELIFKASQALSLTLEKIAARG 459 AVGD MII+PPL +T +IDE++ + L TL+ + + G Sbjct: 436 AVGDRMIIAPPLVMTHAQIDEMMALIVRCLDATLDDLRSAG 476 Lambda K H 0.321 0.137 0.408 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: 671 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 460 Length of database: 479 Length adjustment: 33 Effective length of query: 427 Effective length of database: 446 Effective search space: 190442 Effective search space used: 190442 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 Apr 09 2024. 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