Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 6937531 Sama_1687 para-aminobenzoate synthase, component I (RefSeq)
Query= curated2:Q9X6J4 (508 letters) >FitnessBrowser__SB2B:6937531 Length = 471 Score = 242 bits (617), Expect = 2e-68 Identities = 154/450 (34%), Positives = 232/450 (51%), Gaps = 19/450 (4%) Query: 46 LLESKDDESPWARYSFIGVAPFLTLESETGETFLIKDENGNVQMTASTLKEAFQAVERAL 105 LL+S D A + + AP TL+ + L N T+ Q+V+ AL Sbjct: 40 LLDSADAPHMDAHWDILVAAPVATLKVYESHSELTYAGNTLRLDTSECPFSQLQSVQHAL 99 Query: 106 CVKPLAEAAPFTGGAVGFLGYDFISAIEKVPRHRAPDLAMKAGHFVFCESLFAFDHEKRE 165 + PF GGA+G YD IE++P D+ + F + ++ Sbjct: 100 FSVQKNTSLPFAGGALGSFNYDLGRRIERLPSTALDDINLPLACIGFYDWALMRSYQSDS 159 Query: 166 LSLIHYIRLKGHETMQEKIAIYRAAEERIAALAAKASRPRAEQPLLPAEDEAERAALFSK 225 L+HY+ G + + E +A ++R A A S +L ++ Sbjct: 160 WQLVHYL---GDDALNETLAWLE--QQRDFAQAGAESNTSF--------------SLLTE 200 Query: 226 ASSNYEKEQFLRDVEAVKQYIAAGDVFQAVLSQRFSVPVQAGGFAIYRILRHINPSPYMF 285 + ++Q+ + V+ Y+A+GD +Q L+QRFS Q + Y LR N +P+ Sbjct: 201 FTPQITRDQYQQKFNQVQSYLASGDCYQINLTQRFSADYQGSEWQAYLKLRSANVAPFSA 260 Query: 286 YFRLDGIEIVGSSPEKLIQVRNRRAEIDPIAGTRRRGRSPAEDEKLADELYHDPKERAEH 345 + RL+ I+ SPE+ I++ R+ E PI GT R P D+ A L PK+RAE+ Sbjct: 261 FVRLEEGAILSISPERFIKLDGRQVETKPIKGTLPRLPDPDADKTNAILLKASPKDRAEN 320 Query: 346 YMLVDLARNDIGRVAKYGTVEVPVLMEIGKFSHVMHLISKVVGVLDDDIHPIDALLAAFP 405 M+VDL RNDIGRVA G+V VP L E+ F V HL+S V L ++ D L AAFP Sbjct: 321 LMIVDLLRNDIGRVASPGSVRVPKLFEVESFPAVHHLVSTVTAQLAENKDAFDLLRAAFP 380 Query: 406 AGTVSGAPKVRAMQILQELEPTARGLYAGAIAYIGFDGSIDSCIAIRTAVIKDGYAYVQA 465 G+++GAPK+RAM+I++ELEP+ R +Y G+I YI G++D+ I IRT DG Y A Sbjct: 381 GGSITGAPKIRAMEIIEELEPSRRSIYCGSIGYISQHGNMDTSITIRTLAAVDGKLYCWA 440 Query: 466 GAGIVADSVPELEWKETRNKASALIYAIEQ 495 G G+VADS+ + E++ET +K S ++ +EQ Sbjct: 441 GGGVVADSIADSEYQETFDKISRILPILEQ 470 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: 452 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: 508 Length of database: 471 Length adjustment: 34 Effective length of query: 474 Effective length of database: 437 Effective search space: 207138 Effective search space used: 207138 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: 52 (24.6 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