Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate BWI76_RS18925 BWI76_RS18925 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Koxy:BWI76_RS18925 Length = 434 Score = 345 bits (886), Expect = 2e-99 Identities = 195/424 (45%), Positives = 265/424 (62%), Gaps = 14/424 (3%) Query: 371 QKALSRP-IQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 Q+ L+RP I + I V+ I+ NV+D G++AL EY+ KFD K L E Sbjct: 18 QQLLTRPAISASGSISKTVSEILTNVKDNGDAALREYSAKFD--KTDVKALKVSDEEIAA 75 Query: 430 EG--LTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGG 487 G L++E+K+A+ ++++N+ FH AQ + ++VET PGV C + RPI VGLYIPGG Sbjct: 76 AGARLSDELKQAMAVAVKNIETFHNAQ-QLQAVDVETLPGVRCQQVTRPIASVGLYIPGG 134 Query: 488 TAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQA 547 +A L ST LML PA++A C+++V SPP +D E++Y A+ G I GGAQA Sbjct: 135 SAPLFSTVLMLATPARIAGCQQVVLCSPPPIAD-----EILYAAQLCGVRNIFNVGGAQA 189 Query: 548 VAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDAD 607 +AA+A+GTE++ KVDKI GPGN FVT AK V +IDMPAGPSEVLVIAD A Sbjct: 190 IAALAFGTESVAKVDKIFGPGNAFVTEAKRQVSQRLDG-AAIDMPAGPSEVLVIADSGAT 248 Query: 608 VDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHST 667 DFVASDLLSQAEHG DSQVIL+ + + + AV Q L R + R ++ S Sbjct: 249 PDFVASDLLSQAEHGPDSQVILLTPD--SEMATRVAQAVERQLAALSRAETARGALSASR 306 Query: 668 IVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTN 727 I++ + + +SNQY PEHLI+Q NA + V + +AGSVF+G ++PES GDY+SGTN Sbjct: 307 IIVARDIAQCVAISNQYGPEHLIIQTRNARELVDGITSAGSVFLGDWSPESAGDYASGTN 366 Query: 728 HTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 H LPTYGY S A FQK +T Q ++ +G + + +A E LD H+NAV +R Sbjct: 367 HVLPTYGYTATCSSLGLADFQKRMTVQELSRDGFAALASTIEILAAAERLDAHKNAVTLR 426 Query: 788 MSKL 791 ++ L Sbjct: 427 VAAL 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: 680 Number of extensions: 30 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 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