Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Echvi_2459 Echvi_2459 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Cola:Echvi_2459 Length = 429 Score = 405 bits (1040), Expect = e-117 Identities = 216/421 (51%), Positives = 287/421 (68%), Gaps = 7/421 (1%) Query: 371 QKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFE 430 QK L+RP+QK +I +V PI+ V +G+ AL ++ ++D V++ N +++ E +E Sbjct: 13 QKELARPVQKMKDIQKIVKPIMRKVSRQGDKALKKFALEYDHVEIDNLLVSRDEINEAYE 72 Query: 431 GLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAI 490 + E +K A+ + N+ KFH AQ TE L +E GV C R PI+KVGLYIPGGTA Sbjct: 73 QVDESLKSAIQQAKVNIEKFHKAQ-QTEDLSMEVMEGVTCMRRSVPIQKVGLYIPGGTAP 131 Query: 491 LPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAA 550 L ST LMLG+PA +A C+EIV +PP K +GK+ P ++Y A +G KIV AGGAQA+AA Sbjct: 132 LFSTVLMLGIPANIAGCEEIVLCTPPNK-EGKIHPAILYTANLIGIDKIVKAGGAQAIAA 190 Query: 551 MAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDF 610 + YGTE++P+V KI GPGNQ+VTAAK Q T+ +IDMPAGPSEVLV ADE A F Sbjct: 191 LTYGTESVPQVAKIFGPGNQYVTAAK---QLATKKGIAIDMPAGPSEVLVYADESAVPAF 247 Query: 611 VASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVL 670 VA+DLLSQAEHGIDSQVILV + K ++ V Q +LPR DI +K + +S V+ Sbjct: 248 VAADLLSQAEHGIDSQVILVAT--ASKVAKKTLKEVDKQLAKLPRKDIAKKALENSIAVV 305 Query: 671 CDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTL 730 E+A+ + N YAPEHLI+ +AN ++ V + NAGSVF+G +TPES GDY+SGTNHTL Sbjct: 306 MGNQEKAIALINDYAPEHLIINVANEDEVVANIVNAGSVFIGNFTPESAGDYASGTNHTL 365 Query: 731 PTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790 PTYG+AR YSG + +F K IT Q IT +GL+N+G + +A E LD H+NAV IR+ Sbjct: 366 PTYGFARNYSGVSLDSFVKKITYQKITEKGLQNLGPTIEVMAGNELLDAHKNAVSIRLKY 425 Query: 791 L 791 L Sbjct: 426 L 426 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: 793 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: 429 Length adjustment: 36 Effective length of query: 763 Effective length of database: 393 Effective search space: 299859 Effective search space used: 299859 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