Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_015886749.1 NGR_RS03045 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000018545.1:WP_015886749.1 Length = 458 Score = 343 bits (880), Expect = 7e-99 Identities = 185/452 (40%), Positives = 266/452 (58%), Gaps = 5/452 (1%) Query: 10 SALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYG 69 ++L +D AH +HP K G RV+ A+G + DA G +L+D AGLWCVN GYG Sbjct: 4 NSLIELDRAHLIHPVASYRGHEKLGVRVLASAKGATVTDASGRQLIDGFAGLWCVNAGYG 63 Query: 70 RKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTN 129 +SI +AA Q++ LP+ +F EPAIRLAS++A APG+++ VFFT GS+A D+ Sbjct: 64 HESIVEAATRQMRELPYATGYFGLGSEPAIRLASELAERAPGNLDHVFFTLGGSDAVDST 123 Query: 130 LRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPY 189 +R +R YW +G P + IS + YHGS+ GA L + H +P I Y Sbjct: 124 IRFIRYYWIGRGEPQRDQFISVEQGYHGSSTVGAGLTALPAFHAGFGIPFDWQHKIPSHY 183 Query: 190 WFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKR 249 + P+A + AL K+ E+G ++VAAF AEP QG+GGV++PP + +++ Sbjct: 184 AYRNPVGDDPQAIIDASLAALRQKVEEIGPERVAAFYAEPIQGSGGVLVPPKGWMKAMRQ 243 Query: 250 ILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVA 309 + ++ ILF+ DEVI+GFGRTG FA + PD +T+AKG+TSGY+PMG V + D + Sbjct: 244 LCQELGILFVADEVITGFGRTGPLFACHEDEIVPDFMTVAKGLTSGYVPMGAVFMGDHIY 303 Query: 310 DVLISDGGEFA--HGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLS 367 + G A HG+TYS HPV+AAV LE +++ E E L+D R G L L++L Sbjct: 304 QTIADSAGAGAVGHGYTYSAHPVSAAVGLEVLKLYENE-LLDNGR-KAGARLMAGLESLK 361 Query: 368 AHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI-I 426 HPLVG+VRG GM+ A+ELV DK ++ + E+GLV+RA + ++ Sbjct: 362 DHPLVGDVRGRGMLAAVELVVDKEKKTPLPAKAEPARRIFDRAWENGLVIRAFANGVLGY 421 Query: 427 SPPLCITRDEIDELIFKASQALSLTLEKIAAR 458 +PPLC T EID ++ + + L TLE A R Sbjct: 422 APPLCCTEAEIDGIVERTRKVLDETLEDPAVR 453 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: 591 Number of extensions: 29 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: 460 Length of database: 458 Length adjustment: 33 Effective length of query: 427 Effective length of database: 425 Effective search space: 181475 Effective search space used: 181475 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