Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate WP_004148109.1 KVAR_RS15165 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
Query= SwissProt::P00904 (531 letters) >NCBI__GCF_000025465.1:WP_004148109.1 Length = 531 Score = 999 bits (2582), Expect = 0.0 Identities = 502/531 (94%), Positives = 516/531 (97%) Query: 1 MADILLLDNIDSFTYNLADQLRSNGHNVVIYRNHIPAQTLIERLATMSNPVLMLSPGPGV 60 MADILLLDNIDSFTYNLADQLR+NGHNVVIYRN +PAQ LIERL TM NPVLMLSPGPG Sbjct: 1 MADILLLDNIDSFTYNLADQLRANGHNVVIYRNSVPAQALIERLGTMDNPVLMLSPGPGT 60 Query: 61 PSEAGCMPELLTRLRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF 120 PSEAGCMPELLTR+RGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF Sbjct: 61 PSEAGCMPELLTRMRGKLPIIGICLGHQAIVEAYGGYVGQAGEILHGKASSIEHDGQAMF 120 Query: 121 AGLTNPLPVARYHSLVGSNIPAGLTINAHFNGMVMAVRHDADRVCGFQFHPESILTTQGA 180 AGL NPLPVARYHSLVGSNIPAGLTINA+FNGMVMAVRHDADRVCGFQFHPESILTTQGA Sbjct: 121 AGLANPLPVARYHSLVGSNIPAGLTINANFNGMVMAVRHDADRVCGFQFHPESILTTQGA 180 Query: 181 RLLEQTLAWAQQKLEPANTLQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALV 240 RLLEQTLAWA QKLE NTLQPILEKLYQA+TLSQQESHQLFSAVVRGE+KPEQLAAALV Sbjct: 181 RLLEQTLAWALQKLEHTNTLQPILEKLYQAETLSQQESHQLFSAVVRGEVKPEQLAAALV 240 Query: 241 SMKIRGEHPNEIAGAATALLENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAAC 300 SMK+RGE P EIAGAATALLENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAAC Sbjct: 241 SMKVRGEQPQEIAGAATALLENAAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAAC 300 Query: 301 GLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHA 360 GLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSR ALDELGVCFLFAPKYHTGFRHA Sbjct: 301 GLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRAALDELGVCFLFAPKYHTGFRHA 360 Query: 361 MPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGG 420 MPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGG Sbjct: 361 MPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHSGG 420 Query: 421 MDEVSLHAPTIVAELHDGEIKSYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKG 480 MDEVSLHAPT+VAELH+GEIKSYQLTA+DFGLTPYHQ QLAGGTPEENRDILTRLLQGKG Sbjct: 421 MDEVSLHAPTVVAELHNGEIKSYQLTADDFGLTPYHQAQLAGGTPEENRDILTRLLQGKG 480 Query: 481 DAAHEAAVAANVAMLMRLHGHEDLQANAQTVLEVLRSGSAYDRVTALAARG 531 +AAHEAAVAANVAMLMRLHGHEDL+ANAQ VL+VL SG+AYDRVTALAARG Sbjct: 481 EAAHEAAVAANVAMLMRLHGHEDLKANAQQVLDVLHSGAAYDRVTALAARG 531 Lambda K H 0.318 0.134 0.388 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: 1085 Number of extensions: 22 Number of successful extensions: 1 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: 531 Length of database: 531 Length adjustment: 35 Effective length of query: 496 Effective length of database: 496 Effective search space: 246016 Effective search space used: 246016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_004148109.1 KVAR_RS15165 (bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))
# 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/TIGR01245.hmm # target sequence database: /tmp/gapView.1298.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01245 [M=330] Accession: TIGR01245 Description: trpD: anthranilate phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-132 425.6 0.1 9e-132 425.3 0.1 1.1 1 lcl|NCBI__GCF_000025465.1:WP_004148109.1 KVAR_RS15165 bifunctional anthra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_004148109.1 KVAR_RS15165 bifunctional anthranilate synthase glutamate amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.3 0.1 9e-132 9e-132 1 328 [. 204 528 .. 204 530 .. 0.99 Alignments for each domain: == domain 1 score: 425.3 bits; conditional E-value: 9e-132 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 lekl++ ++Ls++e++ql++++++ge++++q+aA+lv ++v+ge+++eiag+a+al+e+a +++ +++ lcl|NCBI__GCF_000025465.1:WP_004148109.1 204 LEKLYQAETLSQQESHQLFSAVVRGEVKPEQLAAALVSMKVRGEQPQEIAGAATALLENAAPFPR-PDY 271 689************************************************************99.7** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 ++DivGTGGDg+++iNiSTasa+vaaa+G+kvaKhGnrsvssksGs+D+L a+g+nl+++++k++++l lcl|NCBI__GCF_000025465.1:WP_004148109.1 272 LFADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLLAAFGINLDMNADKSRAAL 340 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 +e+g++FlfAPkyh+++++++pvR++L++rt+fN+LGPL+nPa+++l+++Gvys++lv +ae+l+ lg lcl|NCBI__GCF_000025465.1:WP_004148109.1 341 DELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGPLINPAHPPLALIGVYSPELVLPIAETLRVLG 409 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 ++ra vvh+ +g+DE+sl+++t vael++gei++y+l++ dfgl+++++ +l+gg++een ++l+++l+ lcl|NCBI__GCF_000025465.1:WP_004148109.1 410 YQRAAVVHS-GGMDEVSLHAPTVVAELHNGEIKSYQLTADDFGLTPYHQAQLAGGTPEENRDILTRLLQ 477 *********.*********************************************************** PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328 gk++ a++++v++N+a++++++g++ dlk+++++++++++sg+a++ +++l+ lcl|NCBI__GCF_000025465.1:WP_004148109.1 478 GKGEAAHEAAVAANVAMLMRLHGHE-DLKANAQQVLDVLHSGAAYDRVTALA 528 ***********************99.********************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (531 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 16.53 // [ok]
This GapMind analysis is from Apr 10 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