Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate SMc02725 SMc02725 anthranilate synthase
Query= curated2:P22099 (541 letters) >FitnessBrowser__Smeli:SMc02725 Length = 729 Score = 197 bits (502), Expect = 9e-55 Identities = 145/472 (30%), Positives = 238/472 (50%), Gaps = 26/472 (5%) Query: 75 IVDSAVRIVCYGHTVSFHALTENGKNLLTHVNQNVRGEV---ASQFDGETLTLEFIQPCD 131 +VD + I +G ++ A E G+ LL + ++++ L L +P Sbjct: 66 VVDPPLAISSFGRSLWIEAYNERGEVLLALIAEDLKSVADITLGSLAARRLDLTINEPDR 125 Query: 132 TIDEDSRLREASSFDALRLVQHSFDLSSQDKHAIFLGGLFAYDLVANFEPLGDAVAT-NQ 190 E+ R + + F LR V + F S++ + L G F YDL F+ + ++ + Sbjct: 126 VFTEEERSKMPTVFTVLRAVTNLFH--SEEDSNLGLYGAFGYDLAFQFDAIELKLSRPDD 183 Query: 191 CPDYVFYVAETLLVVDHQTESCQLQATLFVDGSQKAALESRIEDIRAQCTSPKRLPDATQ 250 D V ++ + +LVVDH + F + + E + DI + P R D+ Sbjct: 184 QRDMVLFLPDEILVVDHYAAKAWIDRYDFA--RENLSTEGKAADIAPE---PFRSVDS-- 236 Query: 251 VANITAQPSVPDQDFCQIVRDLKEFVVKGDIFQVVPSRRFTLPCPS-PLAAYKELKQSNP 309 I ++ ++V KE +GD+F+VVP ++F C S P LK NP Sbjct: 237 ---IPPHGDHRPGEYAELVVKAKESFRRGDLFEVVPGQKFYERCESRPSEISNRLKAINP 293 Query: 310 SPYMFYMQ-DELFTLFGASPESALKYETDTNQIEIYPIAGTRRRGKRPNGEIDFDLDSRI 368 SPY F++ L GASPE ++ +IE PI+GT +RG P DS Sbjct: 294 SPYSFFINLGNQEYLVGASPEMFVR--VSGRRIETCPISGTIKRGDDPIA------DSEQ 345 Query: 369 ELELRSDKKENAEHMMLVDLARNDVARISQAGTRHVADLLKVDRYSHVMHLVSRVVGQLR 428 L+L + KK+ +E M D+ RND +R+ G+ V +++ YS ++H V + G+LR Sbjct: 346 ILKLLNSKKDESELTMCSDVDRNDKSRVCVPGSVKVIGRRQIEMYSRLIHTVDHIEGRLR 405 Query: 429 DDLDALHAYQACMNMGTLTGAPKIRAMQLIRDVEGARRGSYGGAVGYLTGEGTLDTCIVI 488 DD+DA + + T+TGAPK+ AM+ I E + R YGGA+G + G ++T + + Sbjct: 406 DDMDAFDGFLSHAWAVTVTGAPKLWAMRFIESHEKSPRAWYGGAIGMVGFNGDMNTGLTL 465 Query: 489 RSAYVENGIAQVQAGAGVVFDSDPQAEADETRGKAQAVISAIQAAHSQPANK 540 R+ +++GIA+V+AGA +++DS+P+ E ET KA A+I+AI+ A S + K Sbjct: 466 RTIRIKDGIAEVRAGATLLYDSNPEEEEAETELKASAMIAAIRDAKSANSAK 517 Lambda K H 0.319 0.134 0.381 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: 805 Number of extensions: 41 Number of successful extensions: 6 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: 541 Length of database: 729 Length adjustment: 38 Effective length of query: 503 Effective length of database: 691 Effective search space: 347573 Effective search space used: 347573 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 (21.7 bits) S2: 54 (25.4 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