Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_041590244.1 TERTU_RS13165 aminodeoxychorismate synthase, component I
Query= curated2:Q9Z4W7 (511 letters) >NCBI__GCF_000023025.1:WP_041590244.1 Length = 701 Score = 224 bits (572), Expect = 6e-63 Identities = 172/506 (33%), Positives = 249/506 (49%), Gaps = 42/506 (8%) Query: 29 EEAARATVPHRAAAAALAREHDVVPLHQEF--LDDSVSPVTAFAQLCGPDEAGFLLESVP 86 + +A A+ P + A A + PL F L + P F F L+S Sbjct: 202 DASAAASKPAKPAPVARSGR---APLKVFFRRLASCLQPSLFFKTCFAASNTSFWLDSEC 258 Query: 87 VSGGVARYSYVGHRPVP----LEPTGGDPLTALRSHLARSVAPVP--------------- 127 R+SY+G P LE + L +R+H SV P Sbjct: 259 FRSPQGRFSYMGDAAGPQAEILEYSQQSQLLRVRTHEGESVVATPLFSYLNEQLAERELH 318 Query: 128 --GLP-PFHGGVVGYLGYEAARHFEDLPLAAGPPPGLPESAFLAADDLVVFDHATRRVLL 184 LP PF+ G VGYLGYE D P++ L AD + VFDH + + L Sbjct: 319 NSELPFPFNLGYVGYLGYEMKG---DCGYPVVHRADTPDACLLFADRICVFDHQAQAIYL 375 Query: 185 MTLYRPARESYDDAVARIVRLNR---ALRRAPAP-AAFSGRPLAAATPADHGTQGWTANL 240 + + E D A + ++ + AL + P P A + AA A G + Sbjct: 376 VCV--DLEEEGDRAKQWLHQMEQHLAALSKIPVPDAPHAVDKHVAAANAQSGL--FVPAH 431 Query: 241 TEAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRARPTDLYRHLRATNPSPYMYHLSLG 300 T+ + E +ARA+E + G++++I L+ +LS P P +L+ LRA NP+PY +L Sbjct: 432 TDQAYLELIARAKEMLQRGESYEICLTNQLSAPCEFEPLELFLRLRAENPAPYASYLCFD 491 Query: 301 GGRHVIGASPE--LLVKAEGRTVRTRPLAGTRPRHPDPAEDLRLERELRADEKERAEHVM 358 V+ SPE L + GR V T+P+ GTR R A D ++ EL +EKERAE++M Sbjct: 492 D-LQVVSCSPERFLTIDQCGR-VETKPIKGTRRRASTAAADAQVIVELTENEKERAENLM 549 Query: 359 LVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGRLAEGRDALDALRSAFPAG 418 +VDL RNDLG+V++ G+V V L VE F V + STV L E R A+D +R+ FP G Sbjct: 550 IVDLLRNDLGQVSKVGSVSVPALFTVETFETVHQMVSTVVSELEEERTAVDCVRACFPGG 609 Query: 419 TLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGADGLTDFAIALRTMVVADGHVHVQAGA 478 +++GAPK R +EI+ +LE RGVY GA+G+ +G D++I +R++V G + G Sbjct: 610 SMTGAPKKRTLEILDQLEGRARGVYSGAIGYFALNGSADWSIVIRSLVCLQGRCSLGVGG 669 Query: 479 GIVADSDPAAEFRETLHKSRAMLTAV 504 I SDP AE ET K+ A+L V Sbjct: 670 AITDLSDPRAELEETRIKAEAILRGV 695 Lambda K H 0.319 0.134 0.394 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: 787 Number of extensions: 32 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: 511 Length of database: 701 Length adjustment: 37 Effective length of query: 474 Effective length of database: 664 Effective search space: 314736 Effective search space used: 314736 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: 53 (25.0 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