Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_028310764.1 H566_RS0106265 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000482785.1:WP_028310764.1 Length = 464 Score = 550 bits (1417), Expect = e-161 Identities = 266/454 (58%), Positives = 331/454 (72%), Gaps = 7/454 (1%) Query: 12 LQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRK 71 LQA+D+AH +HPFTD+ LA +G R+I +AEG++I D +G+++LD M+GLWCVNVGYGR Sbjct: 10 LQALDSAHFIHPFTDTKALAAKGARIISKAEGIWITDREGHRILDGMSGLWCVNVGYGRT 69 Query: 72 SIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLR 131 +ADAA+ Q+ LP+YN+FFQ T EP+I LA+K+A L+PG +RVFF+GSGSE NDT LR Sbjct: 70 ELADAAHRQMAELPYYNSFFQTTTEPSILLAAKLAELSPG-FSRVFFSGSGSEGNDTVLR 128 Query: 132 MVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWF 191 +VR YW + G P + TIISR NAYHGSTVAGASLGGM +MH+QG LPIPGI HIDQPYW Sbjct: 129 LVRHYWSVMGQPKRSTIISRWNAYHGSTVAGASLGGMKYMHEQGGLPIPGIAHIDQPYWV 188 Query: 192 GEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRIL 251 G M EAFG A LE KILELG + V AFI EP QGAGGVIIPP SYW EI+RI Sbjct: 189 EHGHGMDREAFGKLAASWLEDKILELGPENVGAFIGEPVQGAGGVIIPPASYWTEIERIC 248 Query: 252 EKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADV 311 KY+IL + DEVI GFGR G+W+ +Q +G KPDL+T AKG+TSGY P+GGV+V DRV + Sbjct: 249 RKYDILIVADEVICGFGRLGSWWGSQRMGFKPDLMTFAKGVTSGYFPLGGVMVGDRVGEA 308 Query: 312 LISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPL 371 ++ GGEF HG+TYSGHPVA AVAL N+ I+E E LV +V TGP L+ L+ HPL Sbjct: 309 IVEKGGEFEHGYTYSGHPVACAVALANLDIIEREGLVQRVAEVTGPRLRKGFAALADHPL 368 Query: 372 VGEVRGMGMVGAIELV------ADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI 425 V E +G V + L AD V F E+ GM+CR+ C ++GLVMRAVGD MI Sbjct: 369 VAEPEALGFVAGLVLAKEKGGPADGPGFVPFAPELGVGMVCRQHCFDNGLVMRAVGDRMI 428 Query: 426 ISPPLCITRDEIDELIFKASQALSLTLEKIAARG 459 ++PPLC+T DE+DEL+ + L T E + ARG Sbjct: 429 VAPPLCMTEDEVDELLRRIRYCLDRTYEDVRARG 462 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: 722 Number of extensions: 26 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: 464 Length adjustment: 33 Effective length of query: 427 Effective length of database: 431 Effective search space: 184037 Effective search space used: 184037 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