Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_013841403.1 DESRU_RS06925 anthranilate synthase component I
Query= BRENDA::P20580 (492 letters) >NCBI__GCF_000215085.1:WP_013841403.1 Length = 507 Score = 419 bits (1078), Expect = e-122 Identities = 246/498 (49%), Positives = 315/498 (63%), Gaps = 20/498 (4%) Query: 4 EEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGL 63 EE+ RL+ + YN IP+ E LAD +TP+SIY KL+ S+LLESV+ G RYS IG Sbjct: 7 EEYCRLSQE-YNLIPVYREYLADTETPVSIYGKLSSGDPSFLLESVEEGTTLARYSFIGT 65 Query: 64 PCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYF 123 C R + + G++ + PL + +RY+ P + GLPRF GG GYF Sbjct: 66 DCFLNFRFHRGRAEFWGSGMKAKLH--GGPLEALRGLLSRYRTPRLAGLPRFTGGAAGYF 123 Query: 124 GYDCVRYVEKRLATCPN--PDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADP---SEE 178 GYD +R++EK PN PDPLG P LM V+VFD++ + IV P + E Sbjct: 124 GYDMIRHLEK----LPNDKPDPLGLPLCQLMFPGTVLVFDHIRRTL-LIVANVPFAGNLE 178 Query: 179 NAYERGQARLEELLERLRQPITPRRGLDLEAAQ--GREP-----AFRASFTREDYENAVG 231 +Y+ +++++ R+ P L +Q RE A +S R ++E AV Sbjct: 179 ESYQEAVKKIDQVAGRIFTPSASPAYSTLPYSQPYAREKLNQVLAANSSMNRREFEEAVT 238 Query: 232 RIKDYILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPE 291 R DYI AGD QVV SQR S+ F P DLYR LR NP+PY+ +FNFGD +VG+SPE Sbjct: 239 RALDYIRAGDIFQVVLSQRFSLPFTGDPFDLYRRLRSINPSPYLTYFNFGDLVLVGASPE 298 Query: 292 VLVRVEDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVS 351 +LVRVE+G V RPIAGTRPRG +E D L ++L+D KE AEHLML+DLGRNDVGRV+ Sbjct: 299 MLVRVEEGKVFTRPIAGTRPRGKDETEDDLLAAEMLADEKERAEHLMLVDLGRNDVGRVA 358 Query: 352 DIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEI 411 G V+V + M +ERYS+VMH+VS G L EG +DAL A PAGT+SGAPKIRAMEI Sbjct: 359 VPGTVEVPQYMQVERYSHVMHLVSEAKGILEEGKDHLDALGACFPAGTVSGAPKIRAMEI 418 Query: 412 IDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWE 471 I+ELEP+ RG Y GAVGY+ + GNMDTAI IRTAV+ G + Q+G GIVADS PA E+E Sbjct: 419 IEELEPLHRGPYAGAVGYVDFAGNMDTAITIRTAVVHRGSAYFQSGAGIVADSDPAKEYE 478 Query: 472 ETINKRRAMFRAVALAEQ 489 ET++K RAM AV A Q Sbjct: 479 ETLHKARAMATAVMAASQ 496 Lambda K H 0.321 0.139 0.408 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: 681 Number of extensions: 32 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: 492 Length of database: 507 Length adjustment: 34 Effective length of query: 458 Effective length of database: 473 Effective search space: 216634 Effective search space used: 216634 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)
Align candidate WP_013841403.1 DESRU_RS06925 (anthranilate synthase component I)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00564.hmm # target sequence database: /tmp/gapView.3449206.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00564 [M=455] Accession: TIGR00564 Description: trpE_most: anthranilate synthase component I Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-172 559.0 0.0 5.5e-172 558.8 0.0 1.0 1 NCBI__GCF_000215085.1:WP_013841403.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841403.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 558.8 0.0 5.5e-172 5.5e-172 1 454 [. 27 491 .. 27 492 .. 0.94 Alignments for each domain: == domain 1 score: 558.8 bits; conditional E-value: 5.5e-172 TIGR00564 1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelr 73 adt+tp+s+y kl++ + sfllEsve++ +l+RyS+ig + +l+++ + g+ ++ ++ +ak ++ +l++lr NCBI__GCF_000215085.1:WP_013841403.1 27 ADTETPVSIYGKLSSGDPSFLLESVEEGTTLARYSFIGTDCFLNFRFHRGR-AEFWGSGMKAKLHGGPLEALR 98 699************99*******************************995.555668888999********* PP TIGR00564 74 kllekaeesedeld..eplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvilie 144 ll++++ +++l + ++gga Gy+gyd++r++ekl++ ++d+l lp + l++ tv+vfDh+++++++++ NCBI__GCF_000215085.1:WP_013841403.1 99 GLLSRYR--TPRLAglPRFTGGAAGYFGYDMIRHLEKLPNDKPDPLGLPLCQLMFPGTVLVFDHIRRTLLIVA 169 *****64..555555567******************************************************* PP TIGR00564 145 narteaers.aeeeaaarleellaelqkeleka..vkaleekkes.........ftsnvekeeyeekvakake 205 n+ + + + +++ea +++++++ ++ +++++ + ++ +++ +s++++ e+ee+v++a + NCBI__GCF_000215085.1:WP_013841403.1 170 NVPFAGNLEeSYQEAVKKIDQVAGRIFTPSASPaySTLPYSQPYAreklnqvlaANSSMNRREFEEAVTRALD 242 *9877776679***************99987664422333333225566788778889999************ PP TIGR00564 206 yikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAG 278 yi+aGdifqvvlSqr++ +++ +pf+lYr+LR++NPSpyl y+++ d+ lvg+SPE+lv+v++ +v trPiAG NCBI__GCF_000215085.1:WP_013841403.1 243 YIRAGDIFQVVLSQRFSLPFTGDPFDLYRRLRSINPSPYLTYFNFGDLVLVGASPEMLVRVEEGKVFTRPIAG 315 ************************************************************************* PP TIGR00564 279 trkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGel 351 tr+RG++++eD+ l++e+ladeKerAEHlmLvDL+RND+g+va +g+vev++++++e+yshvmH+vSe +G l NCBI__GCF_000215085.1:WP_013841403.1 316 TRPRGKDETEDDLLAAEMLADEKERAEHLMLVDLGRNDVGRVAVPGTVEVPQYMQVERYSHVMHLVSEAKGIL 388 ************************************************************************* PP TIGR00564 352 kdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayv 424 +++++ +Dal a++PaGT+sGAPK+rAme+i+elE+ +Rg+Y+Gavgy++f+g++dtai+iRt+v++ g ay+ NCBI__GCF_000215085.1:WP_013841403.1 389 EEGKDHLDALGACFPAGTVSGAPKIRAMEIIEELEPLHRGPYAGAVGYVDFAGNMDTAITIRTAVVHRGSAYF 461 ************************************************************************* PP TIGR00564 425 qAgaGiVaDSdpeaEyeEtlnKakallrai 454 q gaGiVaDSdp +EyeEtl+Ka+a+++a+ NCBI__GCF_000215085.1:WP_013841403.1 462 QSGAGIVADSDPAKEYEETLHKARAMATAV 491 *************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (507 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13.96 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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