Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate YP_001328350.1 Smed_2685 aminodeoxychorismate synthase
Query= curated2:Q9HS66 (488 letters) >NCBI__GCF_000017145.1:YP_001328350.1 Length = 385 Score = 181 bits (460), Expect = 3e-50 Identities = 119/327 (36%), Positives = 173/327 (52%), Gaps = 17/327 (5%) Query: 154 DLRLIAAVPVDEYTP---DGAFEA-GRDRVQSLAAAIRDGDPAVGPPPADSPAPFESVAG 209 + +L P + TP G F+A D ++A + +P + P A P Sbjct: 66 ETKLAPFAPENRETPLMSFGVFDAPAEDHALAVARRRSENEPFLLEPRAGWDFP------ 119 Query: 210 RAAFESRVRRIQDAIRDGDTFQANVSHRLDAPAAVHPVAVFEALRDTNPAPYSGIVEFPG 269 A+ R R+ +R GD +QAN++ + A + P+A F +L + P Y +V G Sbjct: 120 --AYRQRFERLHRHLRQGDCYQANLTMPIQARWSGDPLAAFWSLIERQPVRYGALVALDG 177 Query: 270 VDLVSASPELLLARRGRE-LTTEPIAGTRPRGATPAEDDAARAALRADDKERAEHAMLVD 328 L+S SPEL + T P+ GT RGA+P EDDA AA+RAD+K +AE+ M+VD Sbjct: 178 PVLLSRSPELFFRVDAEGWIETHPMKGTARRGASPKEDDAIIAAMRADEKTQAENRMIVD 237 Query: 329 LERNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEVTGRLRDSCSLRDAIAAVFPGGTIT 388 L RND+ +V+E G++ VP ++ Y V +VS V +L + D AA+FP G++T Sbjct: 238 LLRNDISRVTEVGTLDVPKLFDIETYPTVHQMVSHVRAKLLTDIGIADIFAALFPCGSVT 297 Query: 389 GAPKPRTMALIDTVEATRRGPYTGSLAAIGFDGDATLSITIRTL-VRRAATYHLRVGAGI 447 GAPK R M ++ +E+ R Y G++ I DG S+ IRT+ + VG GI Sbjct: 298 GAPKMRAMEILHDLESGPRDAYCGAIGYIAPDGAMRFSVAIRTISLFPGGEAVFNVGGGI 357 Query: 448 VHDSTPAAEYDETLAKARALVTALGDA 474 V DST AEY+E L KAR A+GDA Sbjct: 358 VFDSTAEAEYEECLLKAR---FAVGDA 381 Lambda K H 0.317 0.135 0.397 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: 464 Number of extensions: 25 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: 488 Length of database: 385 Length adjustment: 32 Effective length of query: 456 Effective length of database: 353 Effective search space: 160968 Effective search space used: 160968 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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