Align Indole-3-glycerol phosphate synthase; Short=IGPS; EC 4.1.1.48 (characterized, see rationale)
to candidate Echvi_2508 Echvi_2508 Indole-3-glycerol phosphate synthase
Query= uniprot:TRPC_BACTN (260 letters) >FitnessBrowser__Cola:Echvi_2508 Length = 272 Score = 236 bits (602), Expect = 4e-67 Identities = 126/256 (49%), Positives = 179/256 (69%), Gaps = 2/256 (0%) Query: 3 DILSEIIANKRFEVDLQKQAISIEQLQEGINEVPASRSMKRALA-SSDSGIIAEFKRRSP 61 +IL +IIA+K+ EV +K + + L+ + SMK+ + + +GIIAEFKR+SP Sbjct: 2 NILDKIIAHKKEEVAERKSLVPTKMLERSVFFENKVVSMKKYVTLPTKTGIIAEFKRKSP 61 Query: 62 SKGWIKQEARPEEIVPSYLAAGASALSILTDEKFFGGSLKDIRTARPLVDVPIIRKDFII 121 SKG I A+ E+ Y+ AGASALS+LTD++FFGGS +D+ TAR PI+RKDFI+ Sbjct: 62 SKGAINSAAKVEKTSIGYMQAGASALSVLTDKEFFGGSNEDLITARKFNFCPILRKDFIV 121 Query: 122 DEYQLYQAKIVGADAVLLIAAALKQEKCQELAEQAHELGLEVLLEIHSAEELP-YINSKI 180 DEYQ+ +AK +GAD +LLIAAAL+ ++ +ELA AH+LGLEVL+E+H EEL +N + Sbjct: 122 DEYQIVEAKSIGADCILLIAAALEPKRLEELAIFAHKLGLEVLMEVHDQEELDRSLNDHL 181 Query: 181 DMIGINNRNLGTFFTDVENSFRLAGQLPQDAVLVSESGISDPEVVKRLRTAGFRGFLIGE 240 D++G+NNR+L TF ++ S+ L GQ+P V +SESGISDP+ + L+ GF GFLIGE Sbjct: 182 DLVGVNNRSLKTFEVSLDTSYDLVGQIPDKFVKISESGISDPQTLVDLKKGGFDGFLIGE 241 Query: 241 TFMKTPQPGETLQNFL 256 FMK+ +P + NF+ Sbjct: 242 NFMKSIRPHQAAYNFM 257 Lambda K H 0.317 0.135 0.368 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: 216 Number of extensions: 11 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: 260 Length of database: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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: 41 (21.7 bits) S2: 47 (22.7 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