Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate AMB_RS19300 AMB_RS19300 threonine-phosphate decarboxylase
Query= reanno::Miya:8500145 (387 letters) >FitnessBrowser__Magneto:AMB_RS19300 Length = 329 Score = 96.7 bits (239), Expect = 9e-25 Identities = 103/304 (33%), Positives = 140/304 (46%), Gaps = 31/304 (10%) Query: 80 RYAQSGNPRLTAAIAAHH-GVPAE-RVVAGNGSDEIIDLIVRVRAVPGVHNVVAFNPCFS 137 R +SG + A+AA VPA RVVAG+GS +I + R+ + P + Sbjct: 49 RLPESGRHQALLAVAARRWSVPANARVVAGSGSQALIQALPRITPPT---EIAILGPTYG 105 Query: 138 IYELQTRLAGVEFRQAPLAADFSFDWDGLMALVDDATAVVFVTTPDNPSGFCPPVADLER 197 + AG R D GL A+ VV V P+NP G DL Sbjct: 106 EHARAWSAAGHRVR----------DVAGLQEAA--ASPVVVVVNPNNPDGRVVAPEDLLD 153 Query: 198 LAHALPA-GCLLVVDEAYMDFCGDESAH-SLLARVDEFPNLAVLRTFSKSFGLAGLRLGY 255 LA A G LLVVDEA+ GDE SL +R+ P L VLR+F K FGLAG+RLG+ Sbjct: 154 LAARQAARGGLLVVDEAF----GDERPELSLTSRLG--PGLVVLRSFGKFFGLAGIRLGF 207 Query: 256 GILPVQLADYLRRVRLPFSVNILAEEAGLAALADDVFRTETLRVISEGRAALTEGLTALG 315 + LA L P+ V+ A E G ALAD V+ T+ + + A L + LT G Sbjct: 208 AVAEEGLAARLTDHLGPWPVSGPAIELGAQALADRVWTEATITRLRDAAARLGDILTRTG 267 Query: 316 CHVYPSKANFVMFRPAPTCKSAAHLFEELLRRGIIIRPLKSYGLPDLLRVSVGSPDENAA 375 +FR A ++ A L+E L R GI++R PD+LR + + + Sbjct: 268 LE---DLGGTFLFRLARHHQAPA-LYERLGRAGILVRAFAF--RPDILRFGLPGSEADEQ 321 Query: 376 FLKA 379 L+A Sbjct: 322 RLRA 325 Lambda K H 0.322 0.138 0.413 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: 326 Number of extensions: 26 Number of successful extensions: 3 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: 387 Length of database: 329 Length adjustment: 29 Effective length of query: 358 Effective length of database: 300 Effective search space: 107400 Effective search space used: 107400 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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