Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_046007843.1 OLEAN_RS02035 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:E4PQZ8_MARAH (273 letters) >NCBI__GCF_000967895.1:WP_046007843.1 Length = 264 Score = 331 bits (849), Expect = 9e-96 Identities = 163/262 (62%), Positives = 208/262 (79%) Query: 9 TPTILRRIVDRKWEEIDERKRQVSIADLKAKARDQPAARGFANALRSRIEQQTPAVIAEI 68 TPTIL++I+D K E+ +R +VS+A++KA+A DQP ARGF A+++++ PAVIAEI Sbjct: 3 TPTILKKILDTKVIEVQQRSAEVSLANMKARAFDQPEARGFYKAMKTKVAAGLPAVIAEI 62 Query: 69 KKASPSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLPVIR 128 KKASPSKG+ R+ F PA IAESYEK GAACLS+LTD+D+FQG E +L RNACS+PVIR Sbjct: 63 KKASPSKGVFREDFNPARIAESYEKAGAACLSILTDKDYFQGSEAFLQQGRNACSIPVIR 122 Query: 129 KDFMVAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEELDDA 188 KDF++ PYQV+E++ I ADCILLI + L+ Q+Q+L G+A E+G+DVLVEVHD +EL A Sbjct: 123 KDFLIDPYQVFEAKVINADCILLIVSALSDMQLQDLAGLATELGMDVLVEVHDEQELHSA 182 Query: 189 LTLTTPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARGIYG 248 L L TPLVGINNRNLHTF+VSL+ T+ L ++I DR+ ITESGI+ R DV AM A+ + Sbjct: 183 LKLDTPLVGINNRNLHTFEVSLENTYALLDQIPADRMVITESGILGRDDVAAMRAKQVNA 242 Query: 249 FLVGESFMRAEEPGQKLQELFF 270 FLVGE+FMRAE PG KL ELFF Sbjct: 243 FLVGEAFMRAEFPGDKLAELFF 264 Lambda K H 0.320 0.136 0.387 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: 268 Number of extensions: 10 Number of successful extensions: 1 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: 273 Length of database: 264 Length adjustment: 25 Effective length of query: 248 Effective length of database: 239 Effective search space: 59272 Effective search space used: 59272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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