Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_015945221.1 DHAF_RS22210 aminodeoxychorismate synthase, component I
Query= curated2:Q9X6J4 (508 letters) >NCBI__GCF_000021925.1:WP_015945221.1 Length = 721 Score = 283 bits (725), Expect = 1e-80 Identities = 179/508 (35%), Positives = 272/508 (53%), Gaps = 47/508 (9%) Query: 26 LADVIEPLQVFANLRE-EAVFLLESKDDESPWARYSFIGVAPFLTLESETGETFLIK--- 81 LA ++P+++ +E E F L+S + RYSF+G PFL S + +K Sbjct: 209 LAIDLQPIELLEAFKESEYPFFLDSGRNYGGLGRYSFMGAFPFLQA-SACRDGVEVKRFA 267 Query: 82 -DENGNVQMTASTLKEAFQAVERALCVKPLAEAA-----------PFTGGAVGFLGYDFI 129 +E G+ + +S + + + A +K L + PF GGAVGF YD Sbjct: 268 GEEEGSKEDLSSLIGQEWLAYPEGESLKILDDLVERYRVPNPTEFPFVGGAVGFWTYDLK 327 Query: 130 SAIEKVPRHRAPDLAMKAGHFVFCESLFAFDHEKRELSLIHYIRLKGHETMQEKIAIYRA 189 +EK+P+ DL + F + + + +DHE R +L+ + E + A+ +A Sbjct: 328 DELEKMPQSGINDLDLPLWRFSWYDGIVVYDHENRRYTLLACGMTESGECRR---ALAQA 384 Query: 190 AEERIAAL--------AAKASRP---RAEQPLLPAE--DEAERAALF------------- 223 ER+ + K P A Q + A + ER+ + Sbjct: 385 RVERLVGVLEGFLEGRGGKGDHPGTAAAYQRQIGARIGTQQERSGTYQGHDESQDMEQPQ 444 Query: 224 SKASSNYEKEQFLRDVEAVKQYIAAGDVFQAVLSQRFSVPVQAGGFAIYRILRHINPSPY 283 + KEQ+L D++ V YI AGD++QA L+QRF P A+Y+ L NP+P+ Sbjct: 445 ERVHYTVSKEQYLLDLQRVIDYIYAGDIYQANLTQRFQFPYTKEPMALYKALHAHNPAPF 504 Query: 284 MFYFRLDGIEIVGSSPEKLIQVRNR-RAEIDPIAGTRRRGRSPAEDEKLADELYHDPKER 342 + + +I+ SSPE+ +Q+ + E PI GTR RG++P EDE A EL K+R Sbjct: 505 AAFLPYEDFQILSSSPERFVQISAQGEIETRPIKGTRPRGKTPEEDEAYARELTESTKDR 564 Query: 343 AEHYMLVDLARNDIGRVAKYGTVEVPVLMEIGKFSHVMHLISKVVGVLDDDIHPIDALLA 402 AE M++DL RND+GR+ +YG+V V L+ + ++ V HL+S +VG L ++ + L A Sbjct: 565 AELTMIIDLQRNDLGRICRYGSVRVTDLIRLEQYPTVWHLVSTIVGKLKPELKTSEILKA 624 Query: 403 AFPAGTVSGAPKVRAMQILQELEPTARGLYAGAIAYIGFDGSIDSCIAIRTAVIKDGYAY 462 FP G+++GAPK+RAM+I++ELEP RGLY G+I Y+GFDG+ D+ I IRT ++KDG AY Sbjct: 625 IFPGGSITGAPKIRAMEIIEELEPYKRGLYTGSIGYMGFDGAWDTNIVIRTILLKDGQAY 684 Query: 463 VQAGAGIVADSVPELEWKETRNKASALI 490 G GIVADSVPE E++E K AL+ Sbjct: 685 FNGGGGIVADSVPEEEYQEALQKVKALL 712 Lambda K H 0.321 0.137 0.390 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: 814 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 508 Length of database: 721 Length adjustment: 37 Effective length of query: 471 Effective length of database: 684 Effective search space: 322164 Effective search space used: 322164 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 (21.9 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