Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 349729 BT0201 histidinol dehydrogenase (NCBI ptt file)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Btheta:349729 Length = 428 Score = 371 bits (953), Expect = e-107 Identities = 208/433 (48%), Positives = 283/433 (65%), Gaps = 7/433 (1%) Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP 418 + ++K K + L RP T + V II VR +G+ A+LEY FD V LS Sbjct: 2 MKLIKYPSKEQWAELLKRPALNTESLFDTVRTIINKVRAEGDKAVLEYEAAFDKVTLSAL 61 Query: 419 VLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIE 478 + + ++ +++E+K A+ L+ N+ FH++Q +VET GV C + IE Sbjct: 62 TVTSEEIQKAEGLISDELKSAITLAKRNIETFHSSQRFVGK-KVETMEGVTCWQKAVGIE 120 Query: 479 KVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASK 538 KVGLYIPGGTA L ST LML VPA++A C+EIV +PP K+ G + P +++ A+ G SK Sbjct: 121 KVGLYIPGGTAPLFSTVLMLAVPAKIAGCREIVLCTPPDKN-GNIHPAILFAAQLAGVSK 179 Query: 539 IVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEV 598 I AGG QA+AAMAYGTE++PKV KI GPGNQ+VTAAK V A IDMPAGPSEV Sbjct: 180 IFKAGGVQAIAAMAYGTESVPKVYKIFGPGNQYVTAAKQLVSLRDVA---IDMPAGPSEV 236 Query: 599 LVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDI 658 V+AD A+ FVA+DLLSQAEHG+DSQ +L+ SEK E+ + V+ Q +LPR +I Sbjct: 237 EVLADASANPVFVAADLLSQAEHGVDSQAMLI--TTSEKLQAEVMEEVNRQLAKLPRREI 294 Query: 659 VRKCIAHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPES 718 K + +S ++L +EALE++N YAPEHLI++ N + + V NAGSVF+G+ TPES Sbjct: 295 AAKSLENSKLILVKDMDEALELTNAYAPEHLIVETENYLEVAERVINAGSVFLGSLTPES 354 Query: 719 CGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLD 778 GDY+SGTNHTLPT GYA+ YSG + +F + IT Q I P+G++ IG A+ +A E LD Sbjct: 355 AGDYASGTNHTLPTNGYAKAYSGVSLDSFIRKITFQEILPQGMKVIGPAIEEMAANELLD 414 Query: 779 GHRNAVKIRMSKL 791 H+NAV +R++ L Sbjct: 415 AHKNAVTVRLNTL 427 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: 706 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 799 Length of database: 428 Length adjustment: 36 Effective length of query: 763 Effective length of database: 392 Effective search space: 299096 Effective search space used: 299096 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