Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_068166979.1 HTA01S_RS02580 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_001592305.1:WP_068166979.1 Length = 467 Score = 332 bits (851), Expect = 2e-95 Identities = 179/453 (39%), Positives = 268/453 (59%), Gaps = 9/453 (1%) Query: 9 ISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGY 68 I+AL A+D AH +HP KRG ++ A+G+++ D KG +LLDA AGLWCVNVGY Sbjct: 10 IAALDALDRAHLIHPVAPWRVHEKRGPNILTGAQGIWLTDGKGQQLLDAFAGLWCVNVGY 69 Query: 69 GRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDT 128 G++S+ AA Q++ LP+ +F + EPAIRLA+K+ ++P + V+ T GSE+ D Sbjct: 70 GQESVVQAAAEQMRQLPYATGYFHFSSEPAIRLAAKLVQISPASLQHVYLTLGGSESVDA 129 Query: 129 NLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQP 188 +R + +Y + G P KK I+ + YHGS+ GA L + H+ DLP+P +I P Sbjct: 130 AVRFIVQYHNAIGKPGKKHFIALERGYHGSSSTGAGLTALPVFHRGFDLPLPTQHYIPSP 189 Query: 189 YWFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIK 248 + +A + AL+AK+ ELG + VAAF EP QG+GGVI+PP + ++ Sbjct: 190 NPYRAANPADGQAIIDASVAALKAKVAELGAENVAAFFCEPIQGSGGVIVPPKGWLKAMR 249 Query: 249 RILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRV 308 +ILF++DEVI+GFGRTG FA G++PDL+T+AKG+TSGY+PMG ++S++V Sbjct: 250 EAARALDILFVVDEVITGFGRTGPMFACDAEGVEPDLMTVAKGLTSGYVPMGATLMSNKV 309 Query: 309 ADVLIS---DGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQT 365 + G HG TYS HPV+AAVALE +R+ EE ++ + + Q L Sbjct: 310 YSAIADGAPKGAPIGHGATYSAHPVSAAVALEVLRLYEEGGVLANGQRVASAFGQG-LDD 368 Query: 366 LSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI 425 L +HPLVG+ R G++GA+ELV+ K + F + + ++G+V RA GD ++ Sbjct: 369 LLSHPLVGDSRHRGLLGALELVSSKSTKAGFDAALDLPNRMAATAYQNGIVFRAFGDNIL 428 Query: 426 -ISPPLCITRDEIDELIFKASQALSLTLEKIAA 457 +P L T + L+F + L TL+ + A Sbjct: 429 GFAPALTFTESDFG-LMF---ERLKKTLDDVLA 457 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: 537 Number of extensions: 17 Number of successful extensions: 3 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: 460 Length of database: 467 Length adjustment: 33 Effective length of query: 427 Effective length of database: 434 Effective search space: 185318 Effective search space used: 185318 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