GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Sphingomonas indica Dd16

Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate WP_085219434.1 B9N75_RS06205 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8YXQ9
         (362 letters)



>NCBI__GCF_900177405.1:WP_085219434.1
          Length = 356

 Score =  248 bits (634), Expect = 1e-70
 Identities = 146/355 (41%), Positives = 201/355 (56%), Gaps = 17/355 (4%)

Query: 3   SSPTSTQESSTSWYLLLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGV 62
           ++P  T  + T+    L +L+ G+ L    A+ L    ++ A+      A+L AL  +G 
Sbjct: 14  ATPPQTDPAETA----LTRLLSGDRLDERAASHLFTALVAGALSETAIAAMLVALRLQGE 69

Query: 63  SADELTGMAEVLQSQSKMGTGENYSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAFVA 122
           +A  L G A  L++          +  P     +   D+CGTGGDGS + N+STA A VA
Sbjct: 70  TAPVLIGAARALRA----------ADAPFPRPDYLFADSCGTGGDGSGSINVSTAAALVA 119

Query: 123 AAYGVPVAKHGNRSASSLTGSADVLEALGVNLGASPEKVQAALQEVGITFLFAPGWHPAL 182
           AA G+PVAKHGNRS +S  GSADVLE LG  L       + AL + G  FLFAP +HP L
Sbjct: 120 AAAGLPVAKHGNRSFTSRCGSADVLETLGAKLDVDASVSRRALDQAGFCFLFAPLYHPGL 179

Query: 183 KAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIVLH 242
           +    +RR L++RTV N+LGP VNP  P  Q++G+    LL  VA+ L  LG Q+A+V+H
Sbjct: 180 RHAGPVRRALKVRTVMNILGPCVNPAEPRVQLLGVADRTLLVPVARTLAALGVQRALVVH 239

Query: 243 GRERLDEAGLGDLTDLAVLSDGELQLTTINPQEVGVTPAPIGALRGGDVQENAEILKAVL 302
           G   LDE  L   T+ A L DGE++   +  ++VG+ P P+ A+ GG  +ENA  LKA+L
Sbjct: 240 G-SGLDEVALHGETEAARLQDGEIETIFLYAEDVGIEPRPMDAIAGGGPEENAARLKALL 298

Query: 303 QGKGTQAQQDAVALNAALALQVAGAVPLLDHAQGVSVAKEILQTGTAWAKLAQLV 357
            GKG+ A+ D VALNA   L  AG     D   GV +A ++L +G A   LA  V
Sbjct: 299 DGKGSAAEADVVALNAGALLMTAGIA--ADFPAGVRLAADVLASGAAGRTLAAFV 351


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: 270
Number of extensions: 9
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: 356
Length adjustment: 29
Effective length of query: 333
Effective length of database: 327
Effective search space:   108891
Effective search space used:   108891
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_085219434.1 B9N75_RS06205 (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.4178818.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-117  377.1   0.1   4.9e-117  376.9   0.1    1.0  1  NCBI__GCF_900177405.1:WP_085219434.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085219434.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.9   0.1  4.9e-117  4.9e-117       2     329 ..      27     352 ..      26     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 376.9 bits;  conditional E-value: 4.9e-117
                             TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 
                                            +ll++  L+e  a +l++++++g +s++ iaA+lvalr +get+  + g+a+alr+    +++ +++ ++D+
  NCBI__GCF_900177405.1:WP_085219434.1  27 TRLLSGDRLDERAASHLFTALVAGALSETAIAAMLVALRLQGETAPVLIGAARALRAADAPFPR-PDYLFADS 98 
                                           689999********************************************************99.7******* PP

                             TIGR01245  75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlf 147
                                           +GTGGDg+ +iN+STa+alvaaaaG++vaKhGnrs++s++GsaDvLe lg++l++++  ++r+l++ g++Flf
  NCBI__GCF_900177405.1:WP_085219434.1  99 CGTGGDGSGSINVSTAAALVAAAAGLPVAKHGNRSFTSRCGSADVLETLGAKLDVDASVSRRALDQAGFCFLF 171
                                           ************************************************************************* PP

                             TIGR01245 148 APkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220
                                           AP yhp+l+++ pvR+ L+vrtv+N+LGP +nPa++++q+lGv+++ l+  +a++l +lgv+ralvvhg +gl
  NCBI__GCF_900177405.1:WP_085219434.1 172 APLYHPGLRHAGPVRRALKVRTVMNILGPCVNPAEPRVQLLGVADRTLLVPVARTLAALGVQRALVVHG-SGL 243
                                           *********************************************************************.*** PP

                             TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaa 293
                                           DE++l+get+ a+l+dgeie+  l +ed g++++++++++gg +eena++lk++l gk++ a++d+v+lNa+a
  NCBI__GCF_900177405.1:WP_085219434.1 244 DEVALHGETEAARLQDGEIETIFLYAEDVGIEPRPMDAIAGGGPEENAARLKALLDGKGSAAEADVVALNAGA 316
                                           ************************************************************************* PP

                             TIGR01245 294 alyvagkakdlkegvelakeaiksgkalekleelva 329
                                           +l++ag a+d+ +gv+la +++ sg+a  +l+++v+
  NCBI__GCF_900177405.1:WP_085219434.1 317 LLMTAGIAADFPAGVRLAADVLASGAAGRTLAAFVE 352
                                           ******************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (356 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: 15.61
//
[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