Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate GFF1894 HP15_1851 para-aminobenzoate synthase, subunit I
Query= curated2:P05378 (462 letters) >FitnessBrowser__Marino:GFF1894 Length = 463 Score = 218 bits (556), Expect = 3e-61 Identities = 120/270 (44%), Positives = 162/270 (60%), Gaps = 1/270 (0%) Query: 188 FQADFSREAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPSPYMG 247 FQ + A+ +V R YI AGD +Q LS S P+ ++AL NP+PY G Sbjct: 189 FQPRQTPVAFRTSVERVRQYIEAGDCYQANLSQEFSGRFVGDPWRAFQALSDANPTPYSG 248 Query: 248 YLDLGEVVLVSASPESLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEH 307 ++ GE ++S SPE L R V T PI GTRPRG+ E D A EL EK++AE+ Sbjct: 249 FIRSGEASIISVSPERFLEIHDRTVTTSPIKGTRPRGRTPETDLVYASELEGSEKDLAEN 308 Query: 308 VMLLDLSRNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLP 367 +M++DL RND+G A G+V+V + +E Y +V HLVS + LA+G TP+ AL P Sbjct: 309 LMIVDLLRNDLGLNAKPGSVKVDKLFALESYKNVHHLVSHIRAELADGVTPMKALFDAFP 368 Query: 368 MGTVSGAPKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVV-AKGWMHVQ 426 G+++GAPKIRAMEII ELEPH RGPY GS Y DG +D + +RT + +G + Sbjct: 369 GGSITGAPKIRAMEIIRELEPHWRGPYCGSIFYRGLDGTLDSNIAIRTMLCDGEGTIRCW 428 Query: 427 AGAGIVADSVPEREYEECWNKARALLKAVE 456 G GIVADS PE EY+E K +L++ +E Sbjct: 429 GGGGIVADSDPEAEYQETLAKVGSLMRFLE 458 Lambda K H 0.321 0.139 0.408 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: 519 Number of extensions: 19 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: 462 Length of database: 463 Length adjustment: 33 Effective length of query: 429 Effective length of database: 430 Effective search space: 184470 Effective search space used: 184470 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: 51 (24.3 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