GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Salinicoccus carnicancri Crm

Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate WP_026090203.1 C792_RS0103170 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8YXQ9
         (362 letters)



>NCBI__GCF_000330705.1:WP_026090203.1
          Length = 339

 Score =  249 bits (636), Expect = 8e-71
 Identities = 139/334 (41%), Positives = 196/334 (58%), Gaps = 12/334 (3%)

Query: 26  ESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGVSADELTGMAEVLQSQSKMGTGEN 85
           E+L   + AE M+  L++ V      A L AL  KG + +E+  + EVL+  +       
Sbjct: 12  ENLEFEEMAEAMEIILNDTVSDSEVAAFLMALKAKGETVEEIAALVEVLRENA------- 64

Query: 86  YSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAFVAAAYGVPVAKHGNRSASSLTGSAD 145
              LPI  +  +++D CGTGGDGS +FNIST  AFV A   V VAKHGNRS +S TGS+D
Sbjct: 65  ---LPIRRTMTNVMDNCGTGGDGSHSFNISTTSAFVLAGANVTVAKHGNRSVTSRTGSSD 121

Query: 146 VLEALGVNLGASPEKVQAALQEVGITFLFAPGWHPALKAVATLRRTLRIRTVFNLLGPLV 205
           VL  LGV L   PE     LQE  I FLFAP  HP L+ +  +R+ LR+ T+FNL+GPL+
Sbjct: 122 VLSELGVALDFGPEDTDLMLQENNIAFLFAPHVHPKLRQIMKVRQDLRVPTIFNLIGPLI 181

Query: 206 NPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIVLHGRERLDEAGLGDLTDLAVLSDGE 265
           NP+    Q +G++    L  +A  +  LG+++AIV++G   +DEA L     +A+L  G 
Sbjct: 182 NPVELDHQFLGIYDRSQLVMMATVMKRLGRKRAIVINGAGHMDEASLAGENHMALLEKGA 241

Query: 266 LQLTTINPQEVGVTPAPIGALRGGDVQENAEILKAVLQGKGTQAQQDAVALNAALALQVA 325
           +      P+ VG+   P+  + GGD  ENAEILK VL+G    AQ+D V LNA L +  A
Sbjct: 242 IYEMKFTPESVGLPTYPLEEIAGGDSCENAEILKNVLEGTAAPAQRDTVLLNAGLGMYAA 301

Query: 326 GAVPLLDHAQGVSVAKEILQTGTAWAKLAQLVYF 359
           GA   ++   G+ +A+E ++TG A AKL  +V +
Sbjct: 302 GAADSIE--AGIELARESIETGNALAKLRNMVKY 333


Lambda     K      H
   0.314    0.130    0.364 

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: 250
Number of extensions: 11
Number of successful extensions: 2
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: 362
Length of database: 339
Length adjustment: 29
Effective length of query: 333
Effective length of database: 310
Effective search space:   103230
Effective search space used:   103230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_026090203.1 C792_RS0103170 (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.76371.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-118  379.7   2.3   7.4e-118  379.6   2.3    1.0  1  NCBI__GCF_000330705.1:WP_026090203.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_026090203.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.6   2.3  7.4e-118  7.4e-118       3     329 ..       7     332 ..       5     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 379.6 bits;  conditional E-value: 7.4e-118
                             TIGR01245   3 klldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDiv 75 
                                           kl  +++L+ ee++++m+ i+++ +sd+++aA+l+al++kget+eeia+l+++lre+a  +++ + ++++D++
  NCBI__GCF_000330705.1:WP_026090203.1   7 KLSARENLEFEEMAEAMEIILNDTVSDSEVAAFLMALKAKGETVEEIAALVEVLRENALPIRR-TMTNVMDNC 78 
                                           78899********************************************************99.59******* PP

                             TIGR01245  76 GTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfA 148
                                           GTGGDg++++NiST+sa+v+a+a v vaKhGnrsv+s+ Gs+DvL++lgv+l+  pe    +l+e++i+FlfA
  NCBI__GCF_000330705.1:WP_026090203.1  79 GTGGDGSHSFNISTTSAFVLAGANVTVAKHGNRSVTSRTGSSDVLSELGVALDFGPEDTDLMLQENNIAFLFA 151
                                           ************************************************************************* PP

                             TIGR01245 149 PkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglD 221
                                           P+ hp+l+++++vR++L v+t+fNl+GPL+nP++ ++q lG+y+++ + ++a v+k+lg kra+v++g++ +D
  NCBI__GCF_000330705.1:WP_026090203.1 152 PHVHPKLRQIMKVRQDLRVPTIFNLIGPLINPVELDHQFLGIYDRSQLVMMATVMKRLGRKRAIVINGAGHMD 224
                                           ************************************************************************* PP

                             TIGR01245 222 EisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaa 294
                                           E sl ge+++a l++g i e++++pe+ gl++++lee++gg+  enae+lk+vleg +  a+rd v+lNa+  
  NCBI__GCF_000330705.1:WP_026090203.1 225 EASLAGENHMALLEKGAIYEMKFTPESVGLPTYPLEEIAGGDSCENAEILKNVLEGTAAPAQRDTVLLNAGLG 297
                                           ************************************************************************* PP

                             TIGR01245 295 lyvagkakdlkegvelakeaiksgkalekleelva 329
                                           +y+ag+a+++++g+ela+e+i++g+al+kl+++v+
  NCBI__GCF_000330705.1:WP_026090203.1 298 MYAAGAADSIEAGIELARESIETGNALAKLRNMVK 332
                                           *******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (339 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.86
//
[ok]

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

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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 (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