Align Histidinol-phosphate aminotransferase 1, chloroplastic; Gene duplicate 1-B protein; Imidazole acetol-phosphate transaminase; Protein EMBRYO DEFECTIVE 2196; Protein HISTIDINE BIOSYNTHESIS 6A; EC 2.6.1.9 (characterized)
to candidate WP_005812326.1 DHAF_RS06560 pyridoxal phosphate-dependent class II aminotransferase
Query= SwissProt::B9DHD3 (417 letters) >NCBI__GCF_000021925.1:WP_005812326.1 Length = 378 Score = 134 bits (337), Expect = 5e-36 Identities = 120/367 (32%), Positives = 181/367 (49%), Gaps = 37/367 (10%) Query: 81 SAQLGRKPEDIVKLDANENPYGPPPEVFEALGNMKFPYV-YPDPQSRRLRDALAQDSGLE 139 SAQ GR ++ + L AN NP+GPP V+EAL + YPDP RRLR +A+ L Sbjct: 10 SAQYGR--QNFIDLSANINPFGPPQGVWEALQKGVANIIHYPDPNYRRLRGKMAEYYALN 67 Query: 140 SEYILVGCGADELIDLIMRCVLDPGEKIIDCPPTFSMYVFDAAVNGAGVIK----VPRNP 195 +E IL+G GA ELI LI+ + K++ P FS Y A GA V K V Sbjct: 68 AEEILLGNGAGELIFLILHGLRP--RKVLIPQPAFSEYERAALACGAEVNKLILGVKGWG 125 Query: 196 DFSLNVDRIAEVVE--LEKPKCIFLTSPNNPDGSIISEDDLLKILEMPIL----VVLDEA 249 + S + E L + + +F+ SP+NP GS +S+ IL + + VVLDE+ Sbjct: 126 ELSFQNEESHREWEQALAENELVFINSPHNPTGSALSKQQFEVILNLALKHQTWVVLDES 185 Query: 250 YIEFSGVESRMK---WVKKYENLIVLRTFSKRAGLAGLRVGYGAFPLSIIEYLWRAKQPY 306 +++F ESR ++++Y NL+VL + +K + GLR+G ++ L + P+ Sbjct: 186 FVDFLEDESRWSGKGYLRRYPNLLVLYSLTKFYAIPGLRLGAVFGAAKLLGRLQDQRDPW 245 Query: 307 NVSVAGEVAALAALSNGKYLEDVRDALVRERERLFGLL------KEVPFLNPYPSYSNFI 360 V+ E A LAAL++ +Y + VR L +E + K+ L Y S NF Sbjct: 246 AVNSLAEEAGLAALADAEYGKRVRRLLQESKESFYRSFAEGRKGKKYWGLRLYSSKVNFA 305 Query: 361 LCEVTSGMDA-----------KKLKEDLAKMGVMVRHY-NSQELKG-YVRVSAGKPEHTD 407 L +V D+ K L ++L K G++VR N L+G Y+RV+ E + Sbjct: 306 LIQVLEAEDSGTDRDDAGKGKKNLIQELGKQGILVRDCGNFAGLEGNYIRVAIKDQESMN 365 Query: 408 VLMECLK 414 L+ K Sbjct: 366 SLLAGFK 372 Lambda K H 0.319 0.138 0.403 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: 377 Number of extensions: 21 Number of successful extensions: 6 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: 417 Length of database: 378 Length adjustment: 31 Effective length of query: 386 Effective length of database: 347 Effective search space: 133942 Effective search space used: 133942 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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