Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_011842151.1 RSPH17029_RS16010 aminotransferase
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000015985.1:WP_011842151.1 Length = 467 Score = 320 bits (819), Expect = 8e-92 Identities = 189/462 (40%), Positives = 262/462 (56%), Gaps = 13/462 (2%) Query: 5 QQDTISALQAMDAA---HHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGL 61 + D +A A+ AA H L P + A L K V+ AEG+Y+ G +L+D AG+ Sbjct: 3 RNDATNAAGAVGAAMRDHILLPAQEMAKLGKSAQPVLTHAEGIYVHTEDGRRLIDGPAGM 62 Query: 62 WCVNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGS 121 WC VGYGR+ I DA Q LP+ + ++ T PA RLA KIA+L PG +NR+FFT Sbjct: 63 WCAQVGYGRREIVDAIAHQAMVLPYASPWYMAT-SPAARLAEKIATLTPGDLNRIFFTTG 121 Query: 122 GSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPG 181 GS A D+ LR Y ++ G P KK II R + YHGST A+ G D+ Sbjct: 122 GSTAVDSALRFSEFYNNVLGRPQKKRIIVRYDGYHGSTALTAACTGRTGNWPNFDIAQDR 181 Query: 182 IVHIDQPYWFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPD 241 I + P G + S EAF Q E +I LG D +AAF+AEP +GGVIIPP Sbjct: 182 ISFLSSPNPRHAG-NRSQEAFLDDLVQEFEDRIESLGPDTIAAFLAEPILASGGVIIPPA 240 Query: 242 SYWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQ-TLGLKPDLITIAKGMTSGYIPMG 300 Y K I EK++IL+I DEV++GFGR G WFA++ G+ PD+IT AKG+TSGY+P+G Sbjct: 241 GYHARFKAICEKHDILYISDEVVTGFGRCGEWFASEKVFGVVPDIITFAKGVTSGYVPLG 300 Query: 301 GVIVSDRVADVLISD---GGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGP 357 G+ +S+ V + + G F +G+TYS PVA A AL NI ++E E +VD+ R + Sbjct: 301 GLAISEAVLARISGENAKGSWFTNGYTYSNQPVACAAALANIELMEREGIVDQAR-EMAD 359 Query: 358 YLQDRLQTLSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVM 417 Y L +L P V E R +G+VG ++ + D + + + E C E GL++ Sbjct: 360 YFAAALASLRDLPGVAETRSVGLVGCVQCLLDPSRADGTAEDKAFTLKIDERCFELGLIV 419 Query: 418 RAVGDTMIISPPLCITRDEIDELIFKASQALSLTLEKIAARG 459 R +GD +ISPPL I+R +IDE++ QA++ E AA G Sbjct: 420 RPLGDLCVISPPLIISRAQIDEMVAIMRQAIT---EVSAAHG 458 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: 517 Number of extensions: 25 Number of successful extensions: 6 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 10 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