Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012041205.1 BBTA_RS04225 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000015165.1:WP_012041205.1 Length = 431 Score = 254 bits (649), Expect = 7e-72 Identities = 164/437 (37%), Positives = 236/437 (54%), Gaps = 12/437 (2%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 PI L A ++ L+ + ++++ I+++V +G++ALLE T KFD ++L Sbjct: 2 PIRLSRAHADFDAQFRQFLAAKRETSADVEAAARAIVDDVAKRGDAALLEATRKFDRLEL 61 Query: 416 SNPVLN--APFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRF 473 + L A E +AL + + + FH QLP + + L R+ Sbjct: 62 TAASLRVTADEIEAAVTACDAATLDALKFARDRIEAFHLKQLPQDQRFTDAAGVELGWRW 121 Query: 474 PRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEK 533 IE GLY+PGGTA PS+ LM +PA+VA +V P DGK++P V+ A Sbjct: 122 SA-IESAGLYVPGGTAAYPSSVLMNAIPAKVAGVSRLVMVVPA--PDGKLNPLVLAAAHL 178 Query: 534 VGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPA 593 G S+I GGAQAVAA+A+GT TI V KI+GPGN +V AAK V IDM A Sbjct: 179 GGVSEIYRVGGAQAVAALAHGTATIAPVVKIVGPGNAYVAAAKRLVFGKV----GIDMIA 234 Query: 594 GPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQL 653 GPSEVLVIAD+ + D++A+DLL+QAEH +Q IL+ S + ++ AV Q L Sbjct: 235 GPSEVLVIADDSGNADWIAADLLAQAEHDASAQSILI--TDSRRLADDVARAVEGQLKTL 292 Query: 654 PRVDIVRKCIAH-STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVG 712 PR I A I+ + ++A+ +++ A EHL + + + + V NAG++F+G Sbjct: 293 PRAQIAGASWADFGAIIEVEDLDQAVPLADAIAAEHLEIMTRDPDAFAARVRNAGAIFLG 352 Query: 713 AYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVA 772 A+TPE+ GDY G+NH LPT AR SG F K + PE L +G A M + Sbjct: 353 AHTPEAIGDYVGGSNHVLPTARSARFSSGLGVLDFMKRTSLLKCGPEQLRALGPAAMTLG 412 Query: 773 KKEGLDGHRNAVKIRMS 789 K EGLD H +V IR++ Sbjct: 413 KAEGLDAHSRSVGIRLN 429 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: 644 Number of extensions: 35 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: 431 Length adjustment: 37 Effective length of query: 762 Effective length of database: 394 Effective search space: 300228 Effective search space used: 300228 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 10 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