Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate SMc02393 SMc02393 histidinol-phosphate aminotransferase
Query= curated2:Q92MG0 (368 letters) >FitnessBrowser__Smeli:SMc02393 Length = 373 Score = 177 bits (449), Expect = 4e-49 Identities = 109/341 (31%), Positives = 173/341 (50%), Gaps = 4/341 (1%) Query: 24 KEHAPGVAKVHKLSSNETPLGASPRAIEAFQKAAFNLERYPDGQANALKEAIAAVHGLNP 83 ++H +A ++ +NE+ G +P + A ++AA + +Y D + + LK+A+A G +P Sbjct: 28 RQHGRKIAA--RIGANESGFGPAPSVLLAIRQAAGDTWKYADPENHDLKQALARHLGTSP 85 Query: 84 ANILCGNGSDELLGLLCHTYLGPGDEGIVTEHGFLVYKIQITASGGTPVTVKERQERVDV 143 ANI G G D LLG + + G + + G+ + + GG VTV +R D+ Sbjct: 86 ANIAIGEGIDGLLGQIVRLVVEAGAPVVTSLGGYPTFNYHVAGHGGRLVTVPYADDREDL 145 Query: 144 DAILAAV-TERTKIVFIANPANPTGTYIPVEEVRRLHAGLPAGVLLVLDAAYAEYVRRND 202 + +LAAV E +V++ANP NP G++ P E V LP LLVLD AY E R D Sbjct: 146 EGLLAAVGRENAPLVYLANPDNPMGSWWPAERVVAFAQALPETTLLVLDEAYCETAPR-D 204 Query: 203 YEAGLELVSSNRNVVMTRTFSKIYGLAGLRIGWMYAPRDVVEALDRVRGPFNLNAAAIAA 262 +E + NV+ RTFSK YGLAG RIG+ + +A D++R F ++ +AA Sbjct: 205 ALPPIESLIDKPNVIRARTFSKAYGLAGARIGYTLSTPGTAQAFDKIRNHFGMSRIGVAA 264 Query: 263 GAAAIRDQAFVAAAVDQNHTWLAKIGQALTDIGLRVTPSVTNFVLIHFPEEAGMSASDAD 322 AA+ DQ ++ + +IG+ D GL PS TNFV + ++A + + D Sbjct: 265 AIAALADQDYLKEVTLKIANSRQRIGRIAADSGLAPLPSATNFVAVDCGKDASYARAIVD 324 Query: 323 AYLTSRGFILRAVGAYGFPNALRMTIGSEEANKGVVAALTE 363 ++ G +R G +R++ + + AAL E Sbjct: 325 RLMSDHGIFIRMPGVAPLNRCIRISTAPDAEMDLLAAALPE 365 Lambda K H 0.319 0.135 0.389 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: 378 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: 368 Length of database: 373 Length adjustment: 30 Effective length of query: 338 Effective length of database: 343 Effective search space: 115934 Effective search space used: 115934 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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