Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein
Query= metacyc::MONOMER-11537 (425 letters) >NCBI__GCF_001294205.1:WP_053937056.1 Length = 400 Score = 233 bits (595), Expect = 6e-66 Identities = 146/396 (36%), Positives = 217/396 (54%), Gaps = 34/396 (8%) Query: 36 VTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKIN 95 V D G+E+IDF GGIAV + GH HP+++AA+TEQ NKL H V EP + L + + Sbjct: 31 VWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHIS-NVFTNEPALALAKTL- 88 Query: 96 AKVPGDFAKKTLLVTTGSEAVENAVKIARAAT------GRAGVIAFTGAYHGRTMMTLGL 149 V FA++ +G+EA E A+K+AR A+ + V++ ++HGRT T+ + Sbjct: 89 --VEHTFAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSFHGRTFFTVSV 146 Query: 150 TGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPV 209 G+ YS G G P GI Y + +AS+E + +D A +IIEP+ Sbjct: 147 GGQP-KYSDGFGPKPAGIEHFKY----------NDLASLEALIDDDT-----ACVIIEPI 190 Query: 210 QGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVTADLTTFAK 269 QGEGG A +EF++ +RALCD+ LLI DEVQ+G GRTG+ +A GV D+ + AK Sbjct: 191 QGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFGVVPDILSTAK 250 Query: 270 SIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVG 329 + GGFP+ + + + G G TY G+P+A A A + + L KA Sbjct: 251 GLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAVAGTAISIITRPETLSGVKAKS 310 Query: 330 ERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAQVVAKARDKGLILL 389 ER+ GL+AI KYPV+ E+R +G +I V+L A V+ A ++G+++L Sbjct: 311 ERIRAGLQAIADKYPVVAEIRGMGLLIGVQL------KAEYAGRSRDVLNAAAEEGVLVL 364 Query: 390 SCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425 + G +V+R L D ++D GLA +E+ FA L Sbjct: 365 AAGP--DVVRFAPSLVISDDEIDAGLARVEKAFARL 398 Lambda K H 0.320 0.137 0.394 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: 446 Number of extensions: 24 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: 425 Length of database: 400 Length adjustment: 31 Effective length of query: 394 Effective length of database: 369 Effective search space: 145386 Effective search space used: 145386 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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