Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__Btheta:350970 Length = 804 Score = 188 bits (477), Expect = 6e-52 Identities = 125/429 (29%), Positives = 211/429 (49%), Gaps = 27/429 (6%) Query: 16 DAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIAD 75 D H HP+T + D ++RA+G I G L++ M+ WC GY + Sbjct: 388 DREHLWHPYTSTTDPLP--VYKVKRADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQ 445 Query: 76 AAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRR 135 AA QL + + F TH+PAI L + L P M ++F+ SGS A + L+M + Sbjct: 446 AAKDQLDKMS-HVMFGGLTHDPAIELGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQ 504 Query: 136 YWDLKGMPSKKTIISRKNAYHGSTVAGASL-GGMGFMHQQGDLPIPGIVHIDQPYWFGEG 194 YW G P K ++ ++ YHG T S+ + MH +P + P +G Sbjct: 505 YWYAAGKPDKNNFVTIRSGYHGDTWNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFDG 564 Query: 195 RDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPF-QGAGGVIIPPDSYWNEIKRILEK 253 E ++ + +E ++AA I EP QGAGG+ Y E +++ ++ Sbjct: 565 EWNPDEIIPLR-------ETIEKHSKELAALILEPIVQGAGGMWFYHPQYLREAEKLCKE 617 Query: 254 YNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLI 313 ++IL I DE+ +GFGRTG FA + G++PD++ I K +T GY+ + V+ S+++AD + Sbjct: 618 HDILLIFDEIATGFGRTGKLFAWEHAGVEPDIMCIGKALTGGYMTLSAVLASNQIADTIS 677 Query: 314 SDGGE-FAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPLV 372 + + F HG T+ G+P+A AVA ++R+L + + V+ L++ L P V Sbjct: 678 NHAPKAFMHGPTFMGNPLACAVACASVRLLLDSGWAENVKR-IEAQLKEELAPARKFPQV 736 Query: 373 GEVRGMGMVGAIELVADKHSMVRFGSEISAGM-LCREACIESGLVMRAVGDTMIISPPLC 431 +VR +G +G I+ +E S M + +E G+ +R G + + PP Sbjct: 737 ADVRILGAIGVIQ------------TERSVSMAYMQRRFVEEGIWVRPFGKLVYLMPPFI 784 Query: 432 ITRDEIDEL 440 I+ +++ +L Sbjct: 785 ISPEQLSKL 793 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: 819 Number of extensions: 29 Number of successful extensions: 5 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: 804 Length adjustment: 37 Effective length of query: 423 Effective length of database: 767 Effective search space: 324441 Effective search space used: 324441 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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