Align Gamma aminobutyrate transaminase 2; Gamma-aminobutyrate transaminase isozyme 2; LeGABA-TP2; SlGABA-T2; EC 2.6.1.96 (characterized)
to candidate 7025360 Shewana3_2520 aminotransferase (RefSeq)
Query= SwissProt::Q84P53 (458 letters) >FitnessBrowser__ANA3:7025360 Length = 452 Score = 153 bits (387), Expect = 1e-41 Identities = 107/359 (29%), Positives = 181/359 (50%), Gaps = 27/359 (7%) Query: 29 IDKAEGSYVYGVNGKKYLDSLSGLWCTVLGGSEPRLIEAASKQLNKSAFYHSFWNRTTKP 88 + A+G + V+G+K +D S W V G P ++ A +QL++ + + F T +P Sbjct: 30 VHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMERQLHQLS-HVMFGGITHEP 88 Query: 89 SLDLAKELINMFTANKMGKVFFTSSGSEANDTQVKLVWYYNNAIGRP-----NKKKIISR 143 ++ L K+L+ M T + KVF SGS A + +K+ Y P K++I++ Sbjct: 89 AITLCKKLLAM-TCEPLTKVFLCDSGSIAVEVAIKMALQYWQGQDLPLAQKAQKQRILTV 147 Query: 144 KNAYHGSTYMTAGLSGLPS-LHLKFDLPPPYILHTDCPHYWNYHLPGETEEEYSTRLANN 202 K YHG T+ + +H F D P + + L + Sbjct: 148 KKGYHGDTFAAMSVCDPEGGMHTMFGEAVTKQCFVDAP-----------QTPFGEPLRQD 196 Query: 203 ----LENLILKEGPETVAAFIAEPVMGGAGVI-IPPATYFEKIQAVLKKYDILFIADEVI 257 ++ ++ ++ PE +AA I EP+M GAG + + Y ++A+ +Y++L I DE+ Sbjct: 197 DLAPMQRILREQHPE-IAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDEIA 255 Query: 258 CGFGRLGTMFGCDKYNIKPDLVSIAKALSGGYIPIGAVLVSEEISKVIMSQSNQLGVFCH 317 GFGR G +F + +I PD++ + KAL+GGYI + A L ++ +++ I SQS GVF H Sbjct: 256 TGFGRTGKLFAYEHADITPDILCLGKALTGGYISLAATLCTDNVAQGI-SQS-PAGVFMH 313 Query: 318 GFTYSGHPVACAVALEALKIYKEKNITEVVNKLSPKLQEGLKAFIDSPIIGEIRGTGLV 376 G T+ G+P+ACA A +L + ++ V + ++Q L ID P + E+R G V Sbjct: 314 GPTFMGNPLACAAACASLDLINQQEWPAQVAAIEQQMQRELADAIDIPSVKEVRVLGAV 372 Lambda K H 0.318 0.136 0.410 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: 462 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 458 Length of database: 452 Length adjustment: 33 Effective length of query: 425 Effective length of database: 419 Effective search space: 178075 Effective search space used: 178075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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