Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Synpcc7942_1334 Synpcc7942_1334 aminodeoxychorismate synthase, subunit I
Query= curated2:Q9Z4W7 (511 letters) >FitnessBrowser__SynE:Synpcc7942_1334 Length = 465 Score = 259 bits (661), Expect = 2e-73 Identities = 173/452 (38%), Positives = 239/452 (52%), Gaps = 20/452 (4%) Query: 65 PVTAFAQLCGPDEAGFLLESVPVSGGVARYSYVGHRPVPLEP-----TGGDPLTALRSHL 119 P AFA D LL+ + +RY+Y+ P + T DP AL + L Sbjct: 21 PQQAFAPFA-QDPHAVLLDLGEPATPESRYAYLCLSPYATQRGDRLVTEADPFQALATSL 79 Query: 120 AR---SVAPVPGLPPFHGGVVGYLGYEAARHFEDLPLAAGPPPGLPESAFLAADDLVVFD 176 A LPPF GG+ G+L YE E LP P LP + D +V D Sbjct: 80 ATVDWQTNSDSDLPPFQGGICGFLSYECGAWLERLPTPKPVEPRLPLWSLSLYDLVVACD 139 Query: 177 HATRRVLLMTLYRPARESYDDAVARIVRLNRALRRAPAPAAFSGRPLAAATPADHGTQGW 236 RR + + P ++ D R RA +R L + +P W Sbjct: 140 RQQRRTWIFSSGLPLQDPRD-------RQQRAEQRLQWVCDRLQSALPSQSPDWQPQADW 192 Query: 237 TANLTEAQFTERVARAREHIAAGDAFQIVLSR--RLSRPLRARPTDLYRHLRATNPSPYM 294 A TEA F + V + + HI AGD FQ L+ R S+P P LYR L +P P+ Sbjct: 193 QALQTEADFCQAVDQVKCHIRAGDIFQANLTTAFRASQPKDLSPWQLYRRLYQLSPEPFS 252 Query: 295 YHLSLGGGRHVIGASPELLVKAE-GRTVRTRPLAGTRPRHPDPAEDLRLERELRADEKER 353 + + GG ++ SPE ++ + V TRP+ GTRPR DPA D +L EL+A EK+R Sbjct: 253 AYFA-GGDFQLLSVSPERFLRLDRDGWVETRPIKGTRPRSADPAHDRQLATELQASEKDR 311 Query: 354 AEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGRLAEGRDALDALRS 413 AE+VM+VDL RNDLGRV P +++V +L ++E + HV HL+S V G+L G A+D LR+ Sbjct: 312 AENVMIVDLLRNDLGRVCRPRSIQVPQLCQLESYEHVHHLTSQVIGQLRSGLTAVDLLRA 371 Query: 414 AFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGADGLTDFAIALRTMVVADGHVH 473 FP G+++GAPKIR+MEII ELEP R Y G+L ++G DG D +I +RT+ ++ G V Sbjct: 372 TFPGGSITGAPKIRSMEIIHELEPIPRQAYCGSLFWLGFDGSLDASILIRTLQISQGQVL 431 Query: 474 VQAGAGIVADSDPAAEFRETLHKSRAMLTAVR 505 QAG GIVADSDP E E K + +L +++ Sbjct: 432 AQAGCGIVADSDPLDECAEMQVKVQPLLRSLQ 463 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: 558 Number of extensions: 26 Number of successful extensions: 4 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: 465 Length adjustment: 34 Effective length of query: 477 Effective length of database: 431 Effective search space: 205587 Effective search space used: 205587 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: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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