Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Caulo:CCNA_03245 Length = 442 Score = 253 bits (645), Expect = 1e-71 Identities = 146/430 (33%), Positives = 227/430 (52%), Gaps = 15/430 (3%) Query: 22 PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81 PF+ ++ K + PR++++A G++ E ++LD +GLWCV G+ R ++ +A KQ Sbjct: 18 PFTPNRRFK-RHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAA 76 Query: 82 ELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQ 141 E+ Y F HP + A ++ I P+G++ +FFT SGSE DT L++ Y +G+ Sbjct: 77 EMDYAPCF-NMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGK 135 Query: 142 PNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWF-GEGGDMTPEE 200 K +I R GYHG G S+GG+ + G+ H+P + G E Sbjct: 136 GTKTRLIGRERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHLPHTHGLPGNTCAKGQPE 195 Query: 201 FGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVAD 260 G A+ LE + + A I EP+ G+ GV+IPP Y R++ I K+DIL + D Sbjct: 196 NGAHLADDLERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLIFD 255 Query: 261 EVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGGD---- 316 EVI GFGR G F ++ +G+ PD++ +AKGLT+ +P G + ++ + + +G D Sbjct: 256 EVITGFGRVGAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAPIE 315 Query: 317 FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVRGV 376 HG+TYS HP+A A L + RE+ + A Y Q + L D V +VR + Sbjct: 316 LFHGYTYSAHPLACAAGLATLETYREDDLFARA-AGLEGYWQDAMHSLADARHVVDVRNL 374 Query: 377 GLLGAIEL-VQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEID 435 GL+ IEL + A AR M + CFD GL++R GD + ++PPL++ K ID Sbjct: 375 GLVAGIELEPRPGAPTAR------AMEVFETCFDEGLLIRVTGDIIALSPPLILEKDHID 428 Query: 436 ELVTKARKCL 445 +V R+ L Sbjct: 429 RMVETIRRVL 438 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: 551 Number of extensions: 27 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: 442 Length adjustment: 33 Effective length of query: 421 Effective length of database: 409 Effective search space: 172189 Effective search space used: 172189 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