Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate 642683611 Cphamn1_1110 L-aspartate aminotransferase apoenzyme (EC 2.6.1.1)
Query= curated2:Q31GD4 (373 letters) >IMG__ChlphaBS1_FD:642683611 Length = 402 Score = 75.1 bits (183), Expect = 3e-18 Identities = 63/210 (30%), Positives = 103/210 (49%), Gaps = 11/210 (5%) Query: 82 DFLQKQPTEIALGNGSNELLELVARIFAGKGDEIIYSQYAFAVYSISTQAVGATGIEVPA 141 DF QKQ I + NG + L +GDE+I + + + GA + V Sbjct: 96 DFSQKQ---IIVSNGGKQTLANALLALCQEGDEVIIPAPFWVSFPEMVRLAGAEPVIVST 152 Query: 142 K-EWGHDL--EAMAEAITDKTKLIYLANPNNPTGTLFTQKEWEAFISKVPSNVIVVL-DE 197 + G+ + E + AITDKTK++ L +P+NP+G ++ ++E A ++ + I VL DE Sbjct: 153 TLDSGYKMSPEQLESAITDKTKVLILNSPSNPSGAVYAEEEVRALMAVLDGREIFVLSDE 212 Query: 198 AYTEYVTHDEYANGLNYLEQYPN-LIVSRTFSKAYGLAALRIGYMVANEELIAYINRLRA 256 Y + V ++ + + +IVS SK Y + RIGY+ E LI ++++ Sbjct: 213 MYDQIVYGEKKPFSPARIPGMRDWVIVSNGVSKTYSMTGWRIGYLAGPEWLIDACGKIQS 272 Query: 257 --PFNINHLAQVAAKAALK-DPMFVKKTVD 283 N N +AQ AA AAL D +K+ + Sbjct: 273 QTTSNANSIAQKAALAALTGDQQVIKERTE 302 Lambda K H 0.317 0.134 0.380 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: 318 Number of extensions: 22 Number of successful extensions: 2 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: 373 Length of database: 402 Length adjustment: 30 Effective length of query: 343 Effective length of database: 372 Effective search space: 127596 Effective search space used: 127596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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