Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate WP_011318914.1 AVA_RS10755 pyridoxal phosphate-dependent aminotransferase
Query= curated2:Q3AAT6 (362 letters) >NCBI__GCF_000204075.1:WP_011318914.1 Length = 388 Score = 112 bits (280), Expect = 2e-29 Identities = 98/324 (30%), Positives = 162/324 (50%), Gaps = 28/324 (8%) Query: 46 VAAAIKEAVD--KVNYYPDGGAFRLKEKIAAKY------GVTPDNIILGNGSDELVMFLA 97 + AA +A+D K Y G +L+E IA K P+N+I+ NG + L Sbjct: 48 IKAAAAKALDEGKTKYGAAAGEPKLREAIAHKLQKDNHLDYKPENVIVTNGGKHSLYNLI 107 Query: 98 MALIDPGDEAIMPVPSFPRYEPVVTMMNGIAREIPLKE---HRLDLKTMAEAVNEKTRLV 154 +ALIDPGDE I+P P + Y +VT++ G + +P +++ + + +A+ KT+L Sbjct: 108 VALIDPGDEVIIPAPYWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLF 167 Query: 155 YLCNPNNPTGTYITKGELEEFLERVPE-EVVVVLDEAY----FEFARLFNDYPDGLNFFK 209 L +P+NPTG T E++ + V + ++ VV DE Y ++ A+ + G F Sbjct: 168 VLNSPSNPTGMVYTPEEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFN 227 Query: 210 KRPNTVVLRTFSKAYGLAGLRVGYGFAPENLAKAINSLR--PPFNVNFLAQMAAVAALDD 267 + T++ F+KAY + G R+GY P ++ KA +S++ NV AQ A+AAL+D Sbjct: 228 R---TLISNGFAKAYSMTGWRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALED 284 Query: 268 EEYVREVVKNTDEGKKFLYQEIIRM--GLSYI-PSAANFLMIKTEKP--SALVFRELL-- 320 + E ++ ++ + + + GLS P A +L K +L F + L Sbjct: 285 SQDCVEEMRQAFAKRRQVMLDRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIE 344 Query: 321 KRGVIVRSGDIFGMDDWIRVTVGT 344 + V V G FG DD IR++ T Sbjct: 345 EHKVAVIPGIAFGADDNIRLSYAT 368 Lambda K H 0.319 0.139 0.399 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: 324 Number of extensions: 15 Number of successful extensions: 5 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: 362 Length of database: 388 Length adjustment: 30 Effective length of query: 332 Effective length of database: 358 Effective search space: 118856 Effective search space used: 118856 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: 50 (23.9 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