Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 8502101 DvMF_2814 histidinol dehydrogenase (RefSeq)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Miya:8502101 Length = 434 Score = 216 bits (551), Expect = 2e-60 Identities = 144/407 (35%), Positives = 219/407 (53%), Gaps = 16/407 (3%) Query: 388 VNPIIENVRDKGNSALLEYTEKFD--GVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIE 445 V I++ VR G++AL +YT +FD G + + E + + + + + Sbjct: 35 VREILDTVRAGGDAALADYTSRFDCPGFDAARIRVGEDEIAAALEEVGPDDRAIIAEAAA 94 Query: 446 NVRKFHAAQLPTETLEVETQP-GVLCSRFPRPIEKVGLYIPGG---TAILPSTALMLGVP 501 N+R FH AQ E T+P G + + P+++ GLY+PGG L S+ LM +P Sbjct: 95 NIRAFHEAQ--KEQSWFTTRPDGSVLGQMVTPVDRAGLYVPGGQGGNTPLISSLLMNAIP 152 Query: 502 AQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKV 561 AQVA EI SPPRK DG ++P ++ A +G +++ AG A A+AA+A+GTET+ V Sbjct: 153 AQVAGVPEIAVISPPRK-DGTLNPFILAAAHHLGITEVHRAGSAWAIAALAFGTETVRPV 211 Query: 562 DKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEH 621 D I GPGN +VT AK + IDM AGPSE+L++AD A D+VA+D+LSQAEH Sbjct: 212 DVIAGPGNIWVTTAKRLLIGRV----GIDMIAGPSEILILADHTARADWVAADMLSQAEH 267 Query: 622 GIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEALEM 680 D + + S + ++ + Q LPR DI RK +A IV+ + + Sbjct: 268 --DPLASSICITDSPALVDALKLELAAQCDTLPRADIARKALADWGAIVVVPDMATGIGI 325 Query: 681 SNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYS 740 +N+ APEHL + + + + +AG+VF+G ++PE GDY +G NH LPT G AR S Sbjct: 326 TNKVAPEHLEVLTKDPWALLGTIRHAGAVFLGGWSPEPVGDYYAGPNHVLPTMGTARFSS 385 Query: 741 GANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 + TF K + + T ++ +A+ EGL+ H + + R Sbjct: 386 ALSVQTFCKRTSVISATAAFTRGHAASIARLARLEGLEAHARSAESR 432 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: 631 Number of extensions: 31 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: 799 Length of database: 434 Length adjustment: 37 Effective length of query: 762 Effective length of database: 397 Effective search space: 302514 Effective search space used: 302514 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 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