Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_027177759.1 G496_RS0101750 cobyric acid synthase
Query= curated2:Q3AD52 (349 letters) >NCBI__GCF_000429985.1:WP_027177759.1 Length = 880 Score = 125 bits (315), Expect = 3e-33 Identities = 98/327 (29%), Positives = 158/327 (48%), Gaps = 16/327 (4%) Query: 30 ANENPYLFPKSLLEEIFSKIGTRDFPLYPDPLAGRLRIRLSEKLGVLPENIVLGNGSDEL 89 AN NP P L +EI I + YPDP L + EK V P + GNG+ EL Sbjct: 40 ANINPIGPPSWLRQEILHSID--EIECYPDPECSELTLAACEKFSVWPNECIAGNGASEL 97 Query: 90 ILCLYLAFGGYGRIALSFSPSFVMYRHHAFVT--QTEFFEVSYRDDFSLDLDETKKAIEK 147 LC+ GG+ + + P +V Y + + E ++ + F D + +EK Sbjct: 98 -LCIAARLGGFKKAVIPV-PCYVDYERACTLAGLKIEKIQLGMENGFQPDFEAIAAILEK 155 Query: 148 YQPHLVFLANPNNPTGTLVDIETIKKLL--AYDHLLVVDEAYVEFSGVSAIDLLKKYQNL 205 P LVFLA PNNPTGT D +++L + ++DE++ F + K+ +N+ Sbjct: 156 -SPALVFLAQPNNPTGTTFDTGKLRELANRYSESRFIIDESFAAFVEDLDRTVKKRPKNV 214 Query: 206 VILRTFSKARALAGLRLGYLVASVDVVKEIIKVKNPYNVNVFSQIAGEVVLANEEVFQGE 265 + + + +K A+ GLRLG +S ++++++ ++ ++VN+ +Q G L + + + Sbjct: 215 ITIVSLTKFYAIPGLRLGLAFSSPEIIQKMREIMPCWSVNLMAQRVGTRCLKDSDYSELT 274 Query: 266 IKEIVAERERLYNQLASL-GLKPVKSHANFILVE---FGEKAKKIHQELINHGILVRY-- 319 KE R L L+ + GL+ ANF+L + G A I LI++ I VR Sbjct: 275 QKETTRLRNELVAGLSEIPGLRVFPGEANFLLCQVQRVGMNASAIINHLISNKIAVRQCD 334 Query: 320 -LGGALANYLRITVGTPEENRQLLKKL 345 G +Y RI V T ENR L+ +L Sbjct: 335 NFDGLDDSYFRIAVRTDAENRLLVDEL 361 Lambda K H 0.321 0.141 0.398 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: 618 Number of extensions: 32 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: 349 Length of database: 880 Length adjustment: 36 Effective length of query: 313 Effective length of database: 844 Effective search space: 264172 Effective search space used: 264172 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: 53 (25.0 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