GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpD_2 in Pedobacter sp. GW460-11-11-14-LB5

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate CA265_RS05010 CA265_RS05010 anthranilate phosphoribosyltransferase

Query= curated2:A6GWZ4
         (330 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS05010 CA265_RS05010
           anthranilate phosphoribosyltransferase
          Length = 329

 Score =  389 bits (998), Expect = e-113
 Identities = 193/326 (59%), Positives = 253/326 (77%), Gaps = 1/326 (0%)

Query: 1   MKNILNRLINHETLSKQEAKNMLVNISNGSYNPSQIASFLTVYMMRNITINELAGFREAL 60
           MK ILN L  +++ S++EAKN+L++IS G++N SQIA+F+T Y MRNIT+ EL GFR+A+
Sbjct: 1   MKKILNHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAM 60

Query: 61  LELCIPIDLSAYNTIDLCGTGGDGKDTFNISTLASFVTAGAGIKVAKHGNYGVSSISGSS 120
           L++C+ ++LS Y+ IDLCGTGGDGKDTFNISTL+SFV AGAG  VAKHGNYGVSS  GSS
Sbjct: 61  LDMCVKVNLSGYDLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSS 120

Query: 121 NVMENLGIKFSNDPIFLEKCIDQAGICVLHAPLFHPAMKNVAPIRKELAVKTFFNMLGPM 180
           NVME LG  F+N+   L++ +D AGIC LHAPLF+PAMK VAPIRKEL VKTFFNMLGPM
Sbjct: 121 NVMEYLGYTFTNNEDTLKRNLDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPM 180

Query: 181 VNPSFPKNQLVGVFNLELARMYSYLYQNTKTNYTILHSLDGYDEISLTGNTKTITNKMEG 240
           VNP  PK Q+VGVF+LELAR+Y+YLYQ+T  +YTI+H+L+GYDE+SLT + KT +NK E 
Sbjct: 181 VNPGQPKYQMVGVFSLELARLYAYLYQDTDKSYTIVHALEGYDEVSLTCDVKTFSNKGEQ 240

Query: 241 MLKPEDFGVNLLSQTDIQGGTTIQESAQMFVTILSGKGTEAQNNVVCANAGMAIATVNNL 300
           +L  +D G + +    I+GG T++ SA++F+ +L+GK T+ QNNVV  N+ +AI T+   
Sbjct: 241 ILTLQDMGFDKVEVNAIKGGDTVESSAKIFMDVLNGKATDVQNNVVLCNSALAIKTIKPQ 300

Query: 301 NPIQG-FELAKESLLSGKGLETLKKL 325
                 F  A+ESL+S K L + K+L
Sbjct: 301 QSFADCFYEAEESLMSKKALNSFKQL 326


Lambda     K      H
   0.317    0.133    0.375 

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: 370
Number of extensions: 16
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: 330
Length of database: 329
Length adjustment: 28
Effective length of query: 302
Effective length of database: 301
Effective search space:    90902
Effective search space used:    90902
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: 49 (23.5 bits)

Align candidate CA265_RS05010 CA265_RS05010 (anthranilate phosphoribosyltransferase)
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.5233.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    4.2e-93  298.2   0.1    4.8e-93  298.0   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS05010  CA265_RS05010 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS05010  CA265_RS05010 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.0   0.1   4.8e-93   4.8e-93       2     328 ..       6     327 ..       5     329 .] 0.96

  Alignments for each domain:
  == domain 1  score: 298.0 bits;  conditional E-value: 4.8e-93
                                  TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                                ++l++nk+ s+eea++++  i +g ++ +qiaA+++a +++  t++e++g+  a+++  +kv+  + +
  lcl|FitnessBrowser__Pedo557:CA265_RS05010   6 NHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAMLDMCVKVNL-SGY 72 
                                                7899**********************************************************99.5** PP

                                  TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvars 137
                                                +l+D +GTGGDg +t+NiST s++v+a+aG +vaKhGn  vss +Gs++v+e lg+++ ++ + ++r 
  lcl|FitnessBrowser__Pedo557:CA265_RS05010  73 DLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSSNVMEYLGYTFTNNEDTLKRN 140
                                                ******************************************************************** PP

                                  TIGR01245 138 leevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlkn 205
                                                l+  gi+Fl+AP + pa+k vap+RkeLgv+t fN+LGP++nP ++k+q++Gv+s +l++++a   + 
  lcl|FitnessBrowser__Pedo557:CA265_RS05010 141 LDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPMVNPGQPKYQMVGVFSLELARLYAYLYQD 208
                                                ***************************************************************99999 PP

                                  TIGR01245 206 lgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsa.eenaellk 272
                                                   +  ++vh+ +g DE+slt + k  + k ++i    l+ +d+g+++ e++++kgg++ e +a++++
  lcl|FitnessBrowser__Pedo557:CA265_RS05010 209 TDKS-YTIVHALEGYDEVSLTCDVKTFSNKGEQI----LTLQDMGFDKVEVNAIKGGDTvESSAKIFM 271
                                                8877.8999***********98877777776555....6668****************96678999** PP

                                  TIGR01245 273 evlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                                +vl+gk+++ ++++v+ N a a+++ + ++++++ +  a+e+++s+kal+ +++l 
  lcl|FitnessBrowser__Pedo557:CA265_RS05010 272 DVLNGKATDVQNNVVLCNSALAIKTIKPQQSFADCFYEAEESLMSKKALNSFKQLL 327
                                                **************************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (329 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.10
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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