Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= curated2:Q1GP30 (371 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 95.9 bits (237), Expect = 2e-24 Identities = 104/309 (33%), Positives = 138/309 (44%), Gaps = 20/309 (6%) Query: 25 SAGADGRPLIKLSANENPLGTGEKARAAFAAVQSAPDALSRYPDPGSVELRAA----IAA 80 +A G +I LS + T R A A A D P PG ELRAA +A Sbjct: 26 TAKGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDT-HYTPIPGRPELRAALARDVAR 84 Query: 81 KYGL--DPDRVICGNGSDELLHLAAGTYAGPGDEILYVRYGFAVYEIAARRVGA--VPVE 136 + GL +P+ VI G+ L A GDE+L + YE R GA VPV Sbjct: 85 RTGLPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVA 144 Query: 137 ADDRDFATDVDALLAAVTDRTRVVYLANPNNPTGTLATREEVGRLYAGLPQNVLFVI-DQ 195 D D AL AAVT RTR ++LA P NPTG + + EE+ + ++ L+V+ D+ Sbjct: 145 PDAATLRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVADE 204 Query: 196 AYAEYLTPDEDDGGLELAKTRPNVFVT-RTFSKIHGLAAERIGWGYASADVIAALHRIRL 254 YA LT D G+ VT + SK H + R GW A A ++A + + L Sbjct: 205 VYAS-LTFDRPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263 Query: 255 PFNVTRAG---QAAAVAALGDDDFVNRSRAHNARWRAWLAAELESLGN-HGVRVV-PSAT 309 G QAA VA D+ V R R R LE+LG+ G+R + P A Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRR---DIALEALGSVPGLRCLKPEAG 320 Query: 310 NFLLVLFEG 318 F+LV G Sbjct: 321 MFMLVDVRG 329 Lambda K H 0.318 0.135 0.402 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: 397 Number of extensions: 22 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: 371 Length of database: 392 Length adjustment: 30 Effective length of query: 341 Effective length of database: 362 Effective search space: 123442 Effective search space used: 123442 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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