Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate BWI76_RS17865 BWI76_RS17865 aminodeoxychorismate synthase subunit I
Query= curated2:P05378 (462 letters) >FitnessBrowser__Koxy:BWI76_RS17865 Length = 451 Score = 248 bits (633), Expect = 3e-70 Identities = 163/442 (36%), Positives = 237/442 (53%), Gaps = 17/442 (3%) Query: 22 YLKLAEKAPVSFLLES-VERGRQSRFSIVGVGARRTFRLKDGVFTVN-GERVETR--DPL 77 Y P + LL S +RF IV R T + + +N GE V T DPL Sbjct: 19 YFSPLSSQPWAMLLHSGFAEHPHNRFDIVVAQPRATLVTRGNMTVINDGETVSTSAADPL 78 Query: 78 RALYE---RVYAPLERHPDLPPFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEP 134 +++ R + HP LP F GG +G YDL R +E LP+ D+ LPD+ Sbjct: 79 TLVHQQLARFNLQPQAHPQLP-FLGGALGLFGYDLGRRFENLPAQAEADIDLPDMAVGIY 137 Query: 135 EVVAVFDHLKNLLHLVAPGRDPEEAEARLFWAERRLKGPLPGVPGERAGGRARFQADFSR 194 + + DH + + L + G DP+ ARL W E + + P G ++++ SR Sbjct: 138 DWALIVDHQRREVSLFSYG-DPQ---ARLAWLEAQAEPA--AAPFALTSG---WRSNMSR 188 Query: 195 EAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPSPYMGYLDLGEV 254 Y E R+ Y+ +GD +QV L+ R ++ + +R L VN +P+ ++ L E Sbjct: 189 AEYGEKFRQVQAYLHSGDCYQVNLAQRFTASYRGDEWLAFRQLNRVNRAPFSAFIRLQEG 248 Query: 255 VLVSASPESLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLLDLS 314 ++S SPE ++ + TRPI GT PR D E+D A++L K+ AE++M++DL Sbjct: 249 AILSLSPERFIQLRQGEIQTRPIKGTLPRLADPEQDALQAQKLANSAKDRAENLMIVDLM 308 Query: 315 RNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTVSGA 374 RNDIGRVA G+VRV E VE + V HLVSTV L D L + P G+++GA Sbjct: 309 RNDIGRVAVPGSVRVPELFVVEPFPAVHHLVSTVTARLPAHLHAADLLRAAFPGGSITGA 368 Query: 375 PKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAGAGIVAD 434 PK+RAMEII+ELEP RR + GS GYL++ G MD ++T+RT +G ++ AG GIVAD Sbjct: 369 PKVRAMEIIDELEPQRRNAWCGSIGYLSFCGNMDTSITIRTLTACRGRIYCSAGGGIVAD 428 Query: 435 SVPEREYEECWNKARALLKAVE 456 S EY+E ++K +L +E Sbjct: 429 SEEAAEYQETFDKVNRILHQLE 450 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: 478 Number of extensions: 16 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: 451 Length adjustment: 33 Effective length of query: 429 Effective length of database: 418 Effective search space: 179322 Effective search space used: 179322 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