Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_106716615.1 CU100_RS10975 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_003010935.1:WP_106716615.1 Length = 271 Score = 157 bits (397), Expect = 4e-43 Identities = 104/264 (39%), Positives = 145/264 (54%), Gaps = 8/264 (3%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEV--QPSTRHFYDALQGARTA----FILEC 55 M +L KI + K + A K + L + + Q R F ALQ R A I E Sbjct: 1 MVDILRKIESYKREEIAAAKARVRLDELKAQALDQEPPRGFVSALQDKRAAGQFALIAEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHYASA-ISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKG+IR DFDP +A Y+ +A +SVLTD FQG+ +L P L Sbjct: 61 KKASPSKGLIRPDFDPPSLAKAYETGGAACLSVLTDTPSFQGAPEYLKAARAATRLPALR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF+ D YQ+Y AR + AD L++++ + DD + L A M VL EV +E E ER+ Sbjct: 121 KDFLFDTYQVYEARSWGADCILIIMASVTDDAAKALEEAALETGMDVLVEVHDEAELERS 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFANG- 233 + L + ++GINNRDLR S+DL + LA + + ++SESG+ T A L+ G Sbjct: 181 LKLNSPLLGINNRDLRTFSVDLAVSERLARMVPSSKLLVSESGVFTNADCHRLAKCNIGT 240 Query: 234 FLIGSALMAHDDLHAAVRRVLLGE 257 FL+G +LM DD+ A + +L GE Sbjct: 241 FLVGESLMRQDDVATATKTLLQGE 264 Lambda K H 0.320 0.135 0.389 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: 221 Number of extensions: 9 Number of successful extensions: 3 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: 453 Length of database: 271 Length adjustment: 29 Effective length of query: 424 Effective length of database: 242 Effective search space: 102608 Effective search space used: 102608 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: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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