Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 6938546 Sama_2649 beta alanine--pyruvate transaminase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__SB2B:6938546 Length = 446 Score = 296 bits (757), Expect = 1e-84 Identities = 171/438 (39%), Positives = 245/438 (55%), Gaps = 26/438 (5%) Query: 13 TLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDEL 72 T S EH+ PF+ +Q K PR++ +A+G++ D +GN +LD AGLWC G+GR ++ Sbjct: 12 TPSLEHYWMPFTANRQFKAS-PRLLASAEGMFYKDVDGNPVLDSTAGLWCCNAGHGRKKI 70 Query: 73 ADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMV 132 ++A S Q+REL Y F Q HP ELA ++DIAP G+N +FFT SGSE DT L+M Sbjct: 71 SEAVSHQIRELDYAPSF-QMGHPLAFELASRLADIAPAGLNRIFFTNSGSESVDTALKMA 129 Query: 133 RHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQ-GDLPIPGIVHIPQPYWFG 191 Y GQP + I R GYHG G S+GG+ + G+ H+P Sbjct: 130 LAYHRANGQPTRTRFIGRELGYHGVGFGGISVGGIGNNRRTFSQQLLQGVDHLPHTL--- 186 Query: 192 EGGDMTPEEF-------GIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244 D+ F G+ A LE+ I G + + A I EP+ G+ GVI+PP Y Sbjct: 187 ---DIANNAFSRGFPAHGLEKAEVLEQLITLHGAENIAAVIVEPMSGSAGVILPPQGYLK 243 Query: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVR 304 R+++I K+ IL + DEVI GFGR G+ F S +G+ PD+MT AK L +G IPMG + V Sbjct: 244 RLRDITKKHGILLIFDEVITGFGRVGDAFASQRWGVVPDLMTTAKALNNGAIPMGAVFVS 303 Query: 305 DEVVEVLNEGG----DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKR 360 +V + G +F HG+TYSGHPVAAA AL + I +EEK+ E + E Y + Sbjct: 304 QDVHDACMTGPEELIEFFHGYTYSGHPVAAAAALATLDIYQEEKLFERTK-ELEGYWEDA 362 Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDT 420 + L D P V ++R GL+ ++L + R +G + R CF NG ++R GD Sbjct: 363 VHSLRDLPNVIDIRNTGLVAGVQLSPNDEGPGR---RGYKVFER--CFRNGTLVRVTGDI 417 Query: 421 MIIAPPLVITKAEIDELV 438 + ++PPL++ K ID++V Sbjct: 418 IAMSPPLIVEKQHIDQIV 435 Lambda K H 0.320 0.140 0.428 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: 537 Number of extensions: 24 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: 454 Length of database: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 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