GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Lentibacillus jeotgali Grbi

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_010529287.1 ON01_RS01750 anthranilate synthase component I

Query= curated2:Q02001
         (456 letters)



>NCBI__GCF_000224785.1:WP_010529287.1
          Length = 467

 Score =  367 bits (943), Expect = e-106
 Identities = 192/454 (42%), Positives = 290/454 (63%), Gaps = 5/454 (1%)

Query: 3   KIKEISADTMTPISVYLRLKGKNKVILESIPRENDQSRFSIIALNPVKHIKFTDGILSVN 62
           K  +++ADT+TPI +Y  L G+ K +LES  +  ++ ++S I  +P +  K ++   ++ 
Sbjct: 10  KYIKLNADTLTPIGIYENLYGRKKFLLESSIQHKEKGKYSFIGADPYQEFKGSNNATTIL 69

Query: 63  DEI--ISDENPMEFLEKLVCQPESTDENLDLPFTSGAIGYAGFDTYGIFEGIQPELKDSI 120
           + I   S+      L     +    D  L  PF  GA+GY G+D    +E I  EL+D I
Sbjct: 70  NHIRETSENRSEPVLTAFQKEFPKMDAELPFPFFGGAVGYIGYDAIRSYENIGDELRDDI 129

Query: 121 GTPDMYFMLYESALIFDHKREKLIFIEDNTYSQRSEKELQNALSANIESLSLLTEAENEL 180
             PD++ MLY++ +++DH  + +  +  N   Q+ E  L + L+   ++L     A+  +
Sbjct: 130 EMPDVHLMLYQNMIVYDHSNQSVFLVVTNL-DQQPEHVLDDRLAFLKKALIPFPTAD--V 186

Query: 181 TELSKLNFVSNMSQELFEEKVAKAKELIRNGDMFQVVLSQRLTADFTDNPFNYYRKLRVE 240
           +   ++ F   M ++ F   V  AK+ I+NGD++QVVLSQR+ A    +PF +YRKLR  
Sbjct: 187 STGKEVVFEPEMDKQHFMHNVEIAKDHIKNGDIYQVVLSQRMKAAMQGDPFTFYRKLRKV 246

Query: 241 NPSSYMYFMEFDNFHVIGSSPERLVAVHGNQVSTNPIAGTRKRGQTEFEDQALIEDLESD 300
           NPS YM+++ FD++ V+G+SPE L+   G  + TNPIAGTR RG T   D AL  +L +D
Sbjct: 247 NPSPYMFYINFDDYVVLGASPESLIETSGRDIMTNPIAGTRPRGSTTDGDGALRNELLTD 306

Query: 301 PKEVAEHKMLVDLGRNDIGKISKYGSIEVPVFMKVEKYRYVMHITSEVTGELRPEFTAMD 360
            KE++EH+MLVDL RND+G++ +  S+ VP +MKVE Y++VMH+ SEV G+L   FT++D
Sbjct: 307 EKEISEHRMLVDLSRNDLGRVCEIDSVSVPTYMKVENYQHVMHMVSEVHGKLAEGFTSID 366

Query: 361 ALRATLPAGTLSGAPKHRAYQRIYEFETQKRGIYGGAIGYLTKNGNCDFAIAIRTMVLKD 420
           AL A LPAGT+SGAPK RA Q I + E  KRG Y G +GY++ N N + A+AIR++++K+
Sbjct: 367 ALIACLPAGTVSGAPKIRAMQIINDLEKVKRGAYAGGVGYISFNDNLNIALAIRSLIVKE 426

Query: 421 KKAHVQAGAGIVYDSVPEHEYQETLNKAQGLLKV 454
             A++QAGAGIVYDS PE EY ETL+KA+ L++V
Sbjct: 427 NFAYLQAGAGIVYDSDPETEYNETLHKARSLMEV 460


Lambda     K      H
   0.316    0.134    0.374 

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: 584
Number of extensions: 26
Number of successful extensions: 3
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: 456
Length of database: 467
Length adjustment: 33
Effective length of query: 423
Effective length of database: 434
Effective search space:   183582
Effective search space used:   183582
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_010529287.1 ON01_RS01750 (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.2905282.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-178  578.4   0.0   6.8e-178  578.2   0.0    1.0  1  NCBI__GCF_000224785.1:WP_010529287.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010529287.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.2   0.0  6.8e-178  6.8e-178       1     453 [.      16     460 ..      16     462 .. 0.92

  Alignments for each domain:
  == domain 1  score: 578.2 bits;  conditional E-value: 6.8e-178
                             TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelr 73 
                                           adtltpi +y++l   +++fllEs+ +++e+g+yS+ig++p++e+k +++ +++l++  e+++  +    +l 
  NCBI__GCF_000224785.1:WP_010529287.1  16 ADTLTPIGIYENLYG-RKKFLLESSIQHKEKGKYSFIGADPYQEFKGSNNATTILNHIRETSE--NRSEPVLT 85 
                                           69************8.9*******************************996666665555444..33334455 PP

                             TIGR00564  74 kllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkviliena 146
                                           ++ +++ + + el+ p+ ggavGy+gyd +r++e++ +e +d++e+pd++l+l++++iv+Dh +++v+l+ ++
  NCBI__GCF_000224785.1:WP_010529287.1  86 AFQKEFPKMDAELPFPFFGGAVGYIGYDAIRSYENIGDELRDDIEMPDVHLMLYQNMIVYDHSNQSVFLVVTN 158
                                           666666778999************************************************************9 PP

                             TIGR00564 147 rteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakakeyikaGdifqvvlSq 219
                                            +++ +   + +++rl  l + l      ++++ + k++ f+++++k++++++v+ ak++ik+Gdi+qvvlSq
  NCBI__GCF_000224785.1:WP_010529287.1 159 LDQQPE---HVLDDRLAFLKKALIPFP--TADVSTGKEVVFEPEMDKQHFMHNVEIAKDHIKNGDIYQVVLSQ 226
                                           766555...344444444433333222..36677888999********************************* PP

                             TIGR00564 220 rleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDeal 292
                                           r++a ++ +pf +YrkLR+vNPSpy++y++++d+ ++g+SPE+l++++g+++ t+PiAGtr+RG+t++ D al
  NCBI__GCF_000224785.1:WP_010529287.1 227 RMKAAMQGDPFTFYRKLRKVNPSPYMFYINFDDYVVLGASPESLIETSGRDIMTNPIAGTRPRGSTTDGDGAL 299
                                           ************************************************************************* PP

                             TIGR00564 293 eeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraal 365
                                           ++eLl+deKe  EH mLvDL+RND+g+v+++ sv+v+ ++k+e+y+hvmH+vSeV+G+l++++t++Dal+a+l
  NCBI__GCF_000224785.1:WP_010529287.1 300 RNELLTDEKEISEHRMLVDLSRNDLGRVCEIDSVSVPTYMKVENYQHVMHMVSEVHGKLAEGFTSIDALIACL 372
                                           ************************************************************************* PP

                             TIGR00564 366 PaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpea 438
                                           PaGT+sGAPK+rAm++i++lEk+kRg Y+G+vgy+sf+ ++++a+aiR++++k++ ay+qAgaGiV+DSdpe+
  NCBI__GCF_000224785.1:WP_010529287.1 373 PAGTVSGAPKIRAMQIINDLEKVKRGAYAGGVGYISFNDNLNIALAIRSLIVKENFAYLQAGAGIVYDSDPET 445
                                           ************************************************************************* PP

                             TIGR00564 439 EyeEtlnKakallra 453
                                           Ey+Etl+Ka++l+++
  NCBI__GCF_000224785.1:WP_010529287.1 446 EYNETLHKARSLMEV 460
                                           ************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (467 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: 17.85
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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