Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate CA265_RS03630 CA265_RS03630 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Pedo557:CA265_RS03630 Length = 346 Score = 152 bits (384), Expect = 1e-41 Identities = 108/333 (32%), Positives = 172/333 (51%), Gaps = 23/333 (6%) Query: 37 VKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSN 96 V L +NEN G P A RYPD +LK A+S+ GVP + LGNGS+ Sbjct: 30 VFLDANENSYGSPLPAN---------YNRYPDPLQLDLKDAISKIKGVPIENTFLGNGSD 80 Query: 97 DILEIAAHAFVEKGQ-SIVYAQYSFAVYALATQGLGARAIVVPAV-KYGHDLDAMLAAVS 154 + +++ AF G+ +++ ++ +Y ++ V + + D++ + + Sbjct: 81 EAIDLLFRAFCNPGKDNVIVLPPTYGMYEVSANINDVEIRKVSLLPNFQLDMEKIAETID 140 Query: 155 DDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVR 214 +T+LIF+ +PNNPTG I +E L + +VV+DEAY Y Q+ + Sbjct: 141 KNTKLIFICSPNNPTGNSINREDIETILANF--NGIVVVDEAYINYARQKTFIQELT--- 195 Query: 215 RYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKA 274 Y NL+V +TFSKA+GLA LR+G A + ++ D+LN+++ P+N+N Q A AL + A Sbjct: 196 EYGNLVVLQTFSKAWGLAALRLGMAFSSTKVIDVLNKIKPPYNINQATQDLAFEALKNIA 255 Query: 275 FLEKSAALNAQGYRRLTEAFDKLGL--EYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGV 332 + + RL++A L + + PSD NF+L V DA ++ L+ QG+ Sbjct: 256 QVNDWIKESVAERDRLSKALTALNIVKKVYPSDANFILTEV--TDAL--KIYDTLVDQGI 311 Query: 333 IVRPVGNYGLPQ-WLRITIGLPEENEAFIAALE 364 IVR L + LRIT+G EEN+ + LE Sbjct: 312 IVRDRSKVTLCEGCLRITVGTKEENDKLLTVLE 344 Lambda K H 0.318 0.135 0.385 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: 317 Number of extensions: 16 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: 370 Length of database: 346 Length adjustment: 29 Effective length of query: 341 Effective length of database: 317 Effective search space: 108097 Effective search space used: 108097 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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