Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_022950200.1 H035_RS0117255 diaminobutyrate--2-oxoglutarate transaminase
Query= metacyc::MONOMER-11537 (425 letters) >NCBI__GCF_000421465.1:WP_022950200.1 Length = 425 Score = 202 bits (515), Expect = 1e-56 Identities = 142/413 (34%), Positives = 214/413 (51%), Gaps = 17/413 (4%) Query: 18 RGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNK--LT 75 RG + P D+A+ A + D EG+++IDF G VLN GH +PKI A+ E L + + Sbjct: 12 RGYIRAFPAVFDTAQGAHLYDEEGKKYIDFFAGAGVLNYGHNNPKISQALIEYLQRDGIV 71 Query: 76 HTCFQV-LAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIA 134 H + +A ++E K TG+ A E A+K+AR R+ +IA Sbjct: 72 HALDKATVAKRNFMEKFRDTILAPRNMHYKIQFTGPTGTNATEAALKLARMTQKRSNIIA 131 Query: 135 FTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKN 194 FT AYHG TM + +TG G+ F Y N G ++ +I + R + Sbjct: 132 FTNAYHGLTMGAMAVTGNAYYRDESYGVRYNSDFMP-YDNYF-GPDVN-TIDYLRRFLSD 188 Query: 195 DAEPRDI-AAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFF 253 + D+ AAII E VQGEGG +VA E++++L +C + ILLI D++Q G GRTGTFF Sbjct: 189 QSSGVDLPAAIITETVQGEGGIHVASIEWLQQLEQVCREFEILLIVDDIQVGNGRTGTFF 248 Query: 254 AMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVM 313 + E+ G+ D+ +K+I GG P++ + K E +D PG GT+ G+ +A AA + Sbjct: 249 SFERAGIKPDMVALSKAIGGGLPMSLLLMKPE-LDQWQPGEHTGTFRGNNLAFVAATKAL 307 Query: 314 EVFEEEHLLDRCKAVGERLVTGLKAIQAKY-PVIGEVRALGAMIAVELFENGDSHKPNAA 372 E ++++ L K G + LK I KY +I +VR LG + +E N+ Sbjct: 308 EYWDDDELAKAVKHKGAIMEAELKRIAEKYGDIITDVRGLGMVWGLESL--------NSG 359 Query: 373 AVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425 + +A KGL++ G +VL+ L LT +A L +GLAII+E EL Sbjct: 360 LPTDISERAFKKGLVIELAGADDHVLKFLPALTIDEATLREGLAIIDESIGEL 412 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: 407 Number of extensions: 21 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: 425 Length of database: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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 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