Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 16128 b2020 histidinol dehydrogenase (NCBI)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Keio:16128 Length = 434 Score = 361 bits (926), Expect = e-104 Identities = 197/423 (46%), Positives = 271/423 (64%), Gaps = 12/423 (2%) Query: 371 QKALSRPIQKTSE-IMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 ++ L RP SE I VN I++NV+ +G+ AL EY+ KFD ++ ++A Sbjct: 18 RQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAAS 77 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQ-LPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGT 488 E L++E+K+A+ ++++N+ FH AQ LP ++VETQPGV C + RP+ VGLYIPGG+ Sbjct: 78 ERLSDELKQAMAVAVKNIETFHTAQKLPP--VDVETQPGVRCQQVTRPVASVGLYIPGGS 135 Query: 489 AILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAV 548 A L ST LML PA +A CK++V SPP +D E++Y A+ G + GGAQA+ Sbjct: 136 APLFSTVLMLATPASIAGCKKVVLCSPPPIAD-----EILYAAQLCGVQDVFNVGGAQAI 190 Query: 549 AAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADV 608 AA+A+GTE++PKVDKI GPGN FVT AK V +IDMPAGPSEVLVIAD A Sbjct: 191 AALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDG-AAIDMPAGPSEVLVIADSGATP 249 Query: 609 DFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTI 668 DFVASDLLSQAEHG DSQVIL+ + + + +AV Q +LPR + R+ + S + Sbjct: 250 DFVASDLLSQAEHGPDSQVILL--TPAADMARRVAEAVERQLAELPRAETARQALNASRL 307 Query: 669 VLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNH 728 ++ + +E+SNQY PEHLI+Q NA + V + +AGSVF+G ++PES GDY+SGTNH Sbjct: 308 IVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNH 367 Query: 729 TLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 LPTYGY S A FQK +T Q ++ EG + + +A E L H+NAV +R+ Sbjct: 368 VLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRV 427 Query: 789 SKL 791 + L Sbjct: 428 NAL 430 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: 714 Number of extensions: 36 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: 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 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