Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 201372 SO2221 para-aminobenzoate synthase, component I (NCBI ptt file)
Query= curated2:Q9X6J4 (508 letters) >FitnessBrowser__MR1:201372 Length = 467 Score = 242 bits (618), Expect = 2e-68 Identities = 155/459 (33%), Positives = 239/459 (52%), Gaps = 29/459 (6%) Query: 41 EEAVFLLESKDDESPWARYSFIGVAPFLTLESETGETFLIKDENGNVQMTA--STLKEAF 98 E LL+S + A++ I V P TL + GE IK + + + S + F Sbjct: 30 EPWAILLDSANAPHLDAKFDIICVNPIATLITH-GELTEIKVQLPELTIPTQMSATDDPF 88 Query: 99 QAVERAL---CVKPLAEAAPFTGGAVGFLGYDFISAIEKVPRHRAPDLAMKAGHFVFCES 155 V + L + A PF+GGA+G YD +E +P A D+ + + F + Sbjct: 89 TLVNQLLRHWYPQSFACELPFSGGAMGSFSYDLGRRVEAIPNIAAQDIQLGEMNIGFYDW 148 Query: 156 LFAFDHEKRELSLIHYIRLKGHETMQEKIAIYRAAEERIAALAAKASRPRAEQPLLPAED 215 FD++++ L+HY+ G ++ ++ I A + +A Sbjct: 149 ALIFDYQQQCWHLVHYL---GETALETQLKIIEAKMAKTVKIA----------------- 188 Query: 216 EAERAALFSKASSNYEKEQFLRDVEAVKQYIAAGDVFQAVLSQRFSVPVQAGGFAIYRIL 275 L + ++ +K +++ V+ Y+ +GD +Q L+QRF Q ++ Y L Sbjct: 189 ---EFTLVTPWAAQLKKADYVKKFNQVQAYLHSGDCYQINLTQRFEAQYQGDEWSAYCKL 245 Query: 276 RHINPSPYMFYFRLDGIEIVGSSPEKLIQVRNRRAEIDPIAGTRRRGRSPAEDEKLADEL 335 R N +P+ + RL+ I+ SPE+ IQ+R + PI GT R PA D++ A L Sbjct: 246 RSANQAPFSAFMRLNDNTILSISPERFIQLRGDDIQTKPIKGTLPRHNDPALDKQAAQIL 305 Query: 336 YHDPKERAEHYMLVDLARNDIGRVAKYGTVEVPVLMEIGKFSHVMHLISKVVGVLDDDIH 395 + PK+RAE+ M+VDL RNDIG+VA G+V+VP L + F V HL+S V LD Sbjct: 306 ANSPKDRAENVMIVDLLRNDIGKVAAPGSVQVPHLFAVESFPAVHHLVSTVTAKLDPQYQ 365 Query: 396 PIDALLAAFPAGTVSGAPKVRAMQILQELEPTARGLYAGAIAYIGFDGSIDSCIAIRTAV 455 D L AAFP G+++GAPK+RAM+I++ELEP+ R LY G+I YI DG +D+ I IRT V Sbjct: 366 ACDLLRAAFPGGSITGAPKIRAMEIIEELEPSRRSLYCGSIGYISQDGQMDTSITIRTIV 425 Query: 456 IKDGYAYVQAGAGIVADSVPELEWKETRNKASALIYAIE 494 + G Y AG GIVADS + E++E+ +K S ++ +E Sbjct: 426 AERGKLYCWAGGGIVADSDVDAEYQESFDKVSRILPLLE 464 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: 451 Number of extensions: 20 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