Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate WP_013707601.1 DESAC_RS13320 indole-3-glycerol phosphate synthase TrpC
Query= uniprot:E4PQZ8_MARAH (273 letters) >NCBI__GCF_000195295.1:WP_013707601.1 Length = 262 Score = 199 bits (506), Expect = 5e-56 Identities = 108/256 (42%), Positives = 155/256 (60%), Gaps = 3/256 (1%) Query: 13 LRRIVDRKWEEIDERKRQVSIADLKAKARDQPAARGFANALRSRIEQQTPAVIAEIKKAS 72 L RIV K +E + S+ DL+++ +P AL + PA+IAEIKKAS Sbjct: 5 LERIVAAKLQENARLRETTSLKDLRSRWERRPEVLSLKAALDQAL---FPAIIAEIKKAS 61 Query: 73 PSKGILRDPFEPAVIAESYEKGGAACLSVLTDRDFFQGDEDYLVAARNACSLPVIRKDFM 132 PSKG+LR + +A +Y+ GAA +SVLT+R FFQG D+L R +P++RKDF+ Sbjct: 62 PSKGVLRPDLDHIDLACAYQTAGAAGISVLTERQFFQGSPDFLAELRPLIGIPLLRKDFI 121 Query: 133 VAPYQVYESRAIGADCILLIAACLTKDQMQELEGIAHEIGLDVLVEVHDGEELDDALTLT 192 + P QVYES A+GAD +LLIAACL ++ L + +G+ LVEV E+ AL + Sbjct: 122 LEPVQVYESAALGADALLLIAACLPPGALRALLLLTESLGMQALVEVFSAAEMQLALEVG 181 Query: 193 TPLVGINNRNLHTFDVSLDTTFDLHERISQDRLTITESGIMTRSDVEAMTARGIYGFLVG 252 L+GIN+RNLHTF+V ++ +L D + SG+ R+D+E GI FL+G Sbjct: 182 ATLIGINHRNLHTFEVDMNRALELAPLAPADVTLVAASGLNCRADLERFRGSGIKAFLIG 241 Query: 253 ESFMRAEEPGQKLQEL 268 E+ +RA +PG+KL+EL Sbjct: 242 ETLVRAPDPGEKLREL 257 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: 217 Number of extensions: 7 Number of successful extensions: 2 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: 262 Length adjustment: 25 Effective length of query: 248 Effective length of database: 237 Effective search space: 58776 Effective search space used: 58776 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