Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 201230 SO2073 histidinol dehydrogenase (NCBI ptt file)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__MR1:201230 Length = 438 Score = 354 bits (909), Expect = e-102 Identities = 200/428 (46%), Positives = 270/428 (63%), Gaps = 17/428 (3%) Query: 373 ALSR-PIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVL----NAPFPEE 427 AL R P+ S + V I++ V +G++A+ E+ +KFDG +L+N N E Sbjct: 17 ALQRSPLIGDSGLEQSVRAIVDAVASRGDAAIKEFNQKFDGARLANISSANSDNLRLSEH 76 Query: 428 YFEG----LTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLY 483 E ++ E+K A+ ++ N+ FH+AQ +++ETQ GV C PIEKVGLY Sbjct: 77 EIEAASARVSPELKAAIAQAMANIDVFHSAQ-QFRPIDIETQAGVRCELRSEPIEKVGLY 135 Query: 484 IPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAG 543 IPGG+A L ST LML +PA +A C++ V SPP +D +VY A G ++I G Sbjct: 136 IPGGSAPLISTVLMLALPATIAGCEQRVLVSPPPINDA-----IVYAANVCGITEIYQVG 190 Query: 544 GAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIAD 603 GAQA+AA+A+GTETIP VDKI GPGN++VT AK V D + SIDMPAGPSEVLVIAD Sbjct: 191 GAQAIAALAFGTETIPSVDKIFGPGNRYVTEAKRLVSQDGRCTVSIDMPAGPSEVLVIAD 250 Query: 604 EDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI 663 DA+ F+A+DLLSQAEHG DSQVILV +L Q + A+ +Q LPR +I + Sbjct: 251 SDANAQFIAADLLSQAEHGPDSQVILVTDSL--PLAQAVNQALKSQLAALPRQEIAATAL 308 Query: 664 AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYS 723 S +L +EA +SN+Y PEHLI+Q + + + AGSVF+GAYTPES GDY+ Sbjct: 309 KGSRTILVKDMQEAALVSNRYGPEHLIIQTRFPREVLNNIRAAGSVFLGAYTPESVGDYA 368 Query: 724 SGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNA 783 SGTNH LPTYGY+R S + A F + T Q ++ +GL +G+AVM +A E LD H+NA Sbjct: 369 SGTNHVLPTYGYSRAVSSLSLADFSRRFTVQELSAKGLLGLGQAVMTLASNELLDAHKNA 428 Query: 784 VKIRMSKL 791 V +R++ L Sbjct: 429 VAVRLASL 436 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: 712 Number of extensions: 34 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: 438 Length adjustment: 37 Effective length of query: 762 Effective length of database: 401 Effective search space: 305562 Effective search space used: 305562 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