Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate SMa0398 SMa0398 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Smeli:SMa0398 Length = 456 Score = 199 bits (505), Expect = 4e-55 Identities = 136/417 (32%), Positives = 196/417 (47%), Gaps = 13/417 (3%) Query: 374 LSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPE--EYFEG 431 L R S + V PI+E VR +G+ AL + + D ++ L E F+ Sbjct: 35 LRRSETDISGFIEKVAPILEAVRTEGDKALARFGRELDKADVTEANLKVTAAEFDAAFKL 94 Query: 432 LTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAIL 491 + + E++ I+N+RKFH Q P E +PG PI+ V LY+P G Sbjct: 95 VDASVLESVQFGIDNIRKFHEEQKPEAMWLKEIRPGAFAGDRFTPIQSVALYVPRGKGSF 154 Query: 492 PSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAM 551 PS +M VPA VA + +PP DG V + A G + AGGAQAVAA+ Sbjct: 155 PSVTMMTSVPAVVAGVPNLAIVTPP-APDGSVDAATLVAARLAGVETVYKAGGAQAVAAV 213 Query: 552 AYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFV 611 AYGTET+ KI+GPG+ +V AAK + +PAGPSEV+++AD+ Sbjct: 214 AYGTETVKPALKIVGPGSPWVVAAK----RSLSGVIDTGLPAGPSEVMILADDTVHGGLA 269 Query: 612 ASDLLSQAEHGIDSQVILV--GVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHST-- 667 A DLL +AEHG DS LV ++E+ + + + H + R + ++ T Sbjct: 270 ALDLLIEAEHGPDSSAYLVTHSGRVAEEALAALPE--HWARMTEQRTAFSKTVLSGKTGG 327 Query: 668 IVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTN 727 IVL EE+ E N YAPEHL L ++ + A + +G +TP S ++S G N Sbjct: 328 IVLTSSIEESYEFVNAYAPEHLELLSEQPFIHLGHITEASEILMGTHTPVSIANFSLGPN 387 Query: 728 HTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAV 784 LPT +AR + + F K + +T R +A EG H AV Sbjct: 388 AVLPTSRWARTFGPLSVTDFVKRSSIGYVTAPAYPEFARHSHNLAIYEGFSSHALAV 444 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: 700 Number of extensions: 33 Number of successful extensions: 4 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: 456 Length adjustment: 37 Effective length of query: 762 Effective length of database: 419 Effective search space: 319278 Effective search space used: 319278 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