Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 5209240 Shew_1718 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__PV4:5209240 Length = 446 Score = 180 bits (456), Expect = 1e-49 Identities = 130/452 (28%), Positives = 214/452 (47%), Gaps = 32/452 (7%) Query: 16 DAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIAD 75 D H HP+T + AEG + G +L+D + W GYG I + Sbjct: 12 DRQHIWHPYTSMTQALP--VYGVVSAEGCELILDDGRRLIDGTSSWWACVHGYGHPYILE 69 Query: 76 AAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRR 135 A QL TL + F TH AI ++ K+ ++ ++ +VF SGS A + ++M + Sbjct: 70 AMQKQLSTLS-HVMFGGITHPSAIAVSKKLLAMTSDNLTKVFLADSGSIAVEVAMKMALQ 128 Query: 136 YWDLKGMPSKKTIISRKNAYHGSTVAGASL----GGMGFMHQQGDLPIPGIVHIDQPYWF 191 YW +G PSK+ I++ K+ YHG T A S+ GGM M + + Q + Sbjct: 129 YWQGRGAPSKQRILTVKHGYHGDTFAAMSVCDPEGGMHTMFGEA---------VTQQLFA 179 Query: 192 GEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPF-QGAGGVIIPPDSYWNEIKRI 250 + E +A+EA +L +AA I EP QGAG + Y ++ + Sbjct: 180 PAPKTPFGETLIADDLEAMEA-LLNAHHQTIAAVIIEPIMQGAGAMHFYSADYLKGLRAL 238 Query: 251 LEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVA- 309 ++Y +L ILDE+ +GFGRTG FA Q G++ D++ + K +T GYI + + SD VA Sbjct: 239 CDRYKVLLILDEIATGFGRTGKLFAYQHAGIEADILCLGKALTGGYISLAATLCSDEVAL 298 Query: 310 DVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAH 369 + S G F HG T+ G+P+A A A ++ ++ + + ++V ++ L T SA Sbjct: 299 GISDSPSGVFMHGPTFMGNPLACAAASASLDLINQHQWPEQVAA-IEQQMKQELATASAI 357 Query: 370 PLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMIISPP 429 V VR +G VG IE+ ++ ++A ++ G+ +R + I PP Sbjct: 358 EGVKAVRCLGAVGVIEMTRSVNTAA-----------LQQAFVDRGVWVRPFSSYIYIMPP 406 Query: 430 LCITRDEIDELIFKASQALSLT-LEKIAARGN 460 I+ ++ L + ++ E A+RG+ Sbjct: 407 YTISAQQLSRLTQAMLEVAAIAGAEAKASRGD 438 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: 520 Number of extensions: 32 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: 446 Length adjustment: 33 Effective length of query: 427 Effective length of database: 413 Effective search space: 176351 Effective search space used: 176351 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 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