Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 7025140 Shewana3_2303 aminodeoxychorismate synthase, subunit I (RefSeq)
Query= curated2:Q9X6J4 (508 letters) >FitnessBrowser__ANA3:7025140 Length = 467 Score = 245 bits (625), Expect = 3e-69 Identities = 141/383 (36%), Positives = 210/383 (54%), Gaps = 23/383 (6%) Query: 115 PFTGGAVGFLGYDFISAIEKVPRHRAPDLAMKAGHFVFCESLFAFDHEKRELSLIHYIRL 174 PF+GGA+G YD IE++P A D+ + + F + FD++++ ++HY+ Sbjct: 108 PFSGGAMGSFSYDLGRRIEQLPSTAAHDIHLGEMNIGFYDWALIFDYQQQSWFMVHYL-- 165 Query: 175 KGHETMQEKIAIYRAAEERIAALAAKASRPRAEQPLLPAEDEAERAALFSKASSNYEKEQ 234 G + ++ I + AK ++P + L S S+ K Q Sbjct: 166 -GDAVLDTQLKI----------IEAKIAKPTKQAEF----------RLTSPWSAQTTKAQ 204 Query: 235 FLRDVEAVKQYIAAGDVFQAVLSQRFSVPVQAGGFAIYRILRHINPSPYMFYFRLDGIEI 294 + V+ Y+ +GD +Q L+QRF Q + Y LR N +P+ + RLD I Sbjct: 205 YAAKFTQVQAYLHSGDCYQINLTQRFEAEYQGDEWRAYCKLRSANQAPFSAFMRLDANAI 264 Query: 295 VGSSPEKLIQVRNRRAEIDPIAGTRRRGRSPAEDEKLADELYHDPKERAEHYMLVDLARN 354 + SPE+ IQ+R + PI GT R P D++ A L H PK+RAE+ M+VDL RN Sbjct: 265 LSISPERFIQLRGDDIQTKPIKGTLPRHSDPMLDKQAAQALAHSPKDRAENVMIVDLLRN 324 Query: 355 DIGRVAKYGTVEVPVLMEIGKFSHVMHLISKVVGVLDDDIHPIDALLAAFPAGTVSGAPK 414 DIG+VA GTV+VP L + F V HL+S V LD H D L AAFP G+++GAPK Sbjct: 325 DIGKVAAPGTVQVPHLFAVESFPAVHHLVSTVTAKLDPHYHACDLLRAAFPGGSITGAPK 384 Query: 415 VRAMQILQELEPTARGLYAGAIAYIGFDGSIDSCIAIRTAVIKDGYAYVQAGAGIVADSV 474 +RAM+I++ELEP+ R LY G++ YI DG +D+ I IRT V + G Y AG GIVADS Sbjct: 385 IRAMEIIEELEPSRRSLYCGSMGYISQDGQMDTSITIRTIVAEQGKLYCWAGGGIVADSN 444 Query: 475 PELEWKETRNKASALIYAIEQAE 497 + E++E+ +K S ++ ++ + Sbjct: 445 VDAEYQESFDKISRILPLLDSPQ 467 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: 462 Number of extensions: 18 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: 467 Length adjustment: 34 Effective length of query: 474 Effective length of database: 433 Effective search space: 205242 Effective search space used: 205242 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