Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate CA265_RS03635 CA265_RS03635 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Pedo557:CA265_RS03635 Length = 426 Score = 399 bits (1026), Expect = e-115 Identities = 218/422 (51%), Positives = 280/422 (66%), Gaps = 8/422 (1%) Query: 367 KVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPE 426 K +++ SR I+ + V II V+ G+ AL + + FD V L L+A + Sbjct: 11 KSKIEELCSRQIEDDKLVEERVTDIISTVKKDGDQALFNFAKAFDKVDLEKLFLDAEELK 70 Query: 427 EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPG 486 + E K+A+D + +N++ FH +QL TE ++ET PGV+C R RPIEKVGLYIPG Sbjct: 71 SIASNIPAEAKKAIDTAYQNIKTFHQSQLKTED-KIETMPGVMCWRESRPIEKVGLYIPG 129 Query: 487 GTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQ 546 GTA+LPST LML PA +A CKEIV SPP+ +DGK + + Y A +G K+ L GGAQ Sbjct: 130 GTAVLPSTFLMLATPAIIAGCKEIVVCSPPQ-NDGKTNCYLAYCAVLLGIEKVFLIGGAQ 188 Query: 547 AVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDA 606 AVAAMA+GTE++P+V KI GPGN++VT AK VQN +IDMPAGPSEVLVIADE A Sbjct: 189 AVAAMAFGTESVPQVYKIFGPGNRYVTTAKTMVQNKV----AIDMPAGPSEVLVIADETA 244 Query: 607 DVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHS 666 + F+A+DLL+QAEHG DSQ ILV S + I E + NQ LPR DI K IA+S Sbjct: 245 NPSFIAADLLAQAEHGTDSQAILVAT--SYQIIAETLKEIENQLNVLPRKDIAAKAIANS 302 Query: 667 TIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGT 726 VL EEA++ SN+YAPEHLIL + + L+ NAGSVF+G TPES GDY+SGT Sbjct: 303 YAVLAKNLEEAMQFSNEYAPEHLILATEHFQSLIPLITNAGSVFLGNLTPESAGDYASGT 362 Query: 727 NHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKI 786 NHTLPT G+A+ YSG +T F K IT Q+++ GL NIGR V +A EGL+ H+NAV I Sbjct: 363 NHTLPTSGFAKAYSGVSTDAFLKKITFQHLSATGLNNIGRTVEILAAAEGLEAHKNAVSI 422 Query: 787 RM 788 R+ Sbjct: 423 RL 424 Lambda K H 0.315 0.133 0.371 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: 756 Number of extensions: 39 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: 799 Length of database: 426 Length adjustment: 36 Effective length of query: 763 Effective length of database: 390 Effective search space: 297570 Effective search space used: 297570 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: 42 (22.0 bits) S2: 53 (25.0 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