GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Desulfotalea psychrophila LSv54

Align Anthranilate synthase component II (characterized, see rationale)
to candidate WP_011188120.1 DP_RS04425 aminodeoxychorismate/anthranilate synthase component II

Query= uniprot:Q8AAD4_BACTN
         (188 letters)



>NCBI__GCF_000025945.1:WP_011188120.1
          Length = 192

 Score =  171 bits (432), Expect = 1e-47
 Identities = 82/185 (44%), Positives = 121/185 (65%)

Query: 2   KILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAGL 61
           KI+LLDN DSFTYN++  ++ +      V+   +++++E++++D II+SPGP +P++   
Sbjct: 5   KIVLLDNNDSFTYNIVDYLRGMTEVQFRVINTHELDIEELDKYDGIIISPGPELPKDFPK 64

Query: 62  LLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLGK 121
           L  +++RY  TK ILG+CLGHQAI + FGA L     V HG   P+ +L+ D LF GL +
Sbjct: 65  LFEVLQRYHRTKPILGICLGHQAIAQFFGADLSQQLPVVHGQAVPMQVLRDDSLFSGLPR 124

Query: 122 EIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQGKEI 181
           E  VG YHSW+V  +  P  L +TA S  G IMA+R     + GIQFHPES +T  G +I
Sbjct: 125 EFRVGLYHSWLVDPKTIPARLVVTALSARGVIMAIRVTDLPIWGIQFHPESHITEHGLKI 184

Query: 182 IKNFL 186
           ++NF+
Sbjct: 185 LENFI 189


Lambda     K      H
   0.319    0.141    0.411 

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: 130
Number of extensions: 3
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: 188
Length of database: 192
Length adjustment: 20
Effective length of query: 168
Effective length of database: 172
Effective search space:    28896
Effective search space used:    28896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 44 (21.6 bits)

Align candidate WP_011188120.1 DP_RS04425 (aminodeoxychorismate/anthranilate synthase component II)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)

# 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/TIGR00566.hmm
# target sequence database:        /tmp/gapView.1259893.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00566  [M=192]
Accession:   TIGR00566
Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.1e-51  160.5   0.0    2.4e-51  160.3   0.0    1.0  1  NCBI__GCF_000025945.1:WP_011188120.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_011188120.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   0.0   2.4e-51   2.4e-51       2     191 ..       6     190 ..       5     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 2.4e-51
                             TIGR00566   2 vllidnydsftynlvqlleelga.evvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 
                                           ++l+dn dsftyn+v++l  +++ +  v   ++l   +ie+l     i+isPGP  P++      e+++++  
  NCBI__GCF_000025945.1:WP_011188120.1   6 IVLLDNNDSFTYNIVDYLRGMTEvQFRVINTHEL---DIEELDKYDGIIISPGPELPKDFPKL-FEVLQRYHR 74 
                                           889***************9998524556666666...556666667799**********9887.9******** PP

                             TIGR00566  74 klPilGvClGhqalaqafGadvvraekvkhGkvseie.hngaavfaglfnPdalkatryhslvveaetldtll 145
                                             PilG+ClGhqa+aq fGad+++   v hG+   ++ + + ++f gl  P+ ++++ yhs  v+++t+++ l
  NCBI__GCF_000025945.1:WP_011188120.1  75 TKPILGICLGHQAIAQFFGADLSQQLPVVHGQAVPMQvLRDDSLFSGL--PREFRVGLYHSWLVDPKTIPARL 145
                                           ************************************845788999999..777******************** PP

                             TIGR00566 146 evtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191
                                            vtal+ +   imair  dlp+ G+qfhPes ++e+G ++l+nf+k
  NCBI__GCF_000025945.1:WP_011188120.1 146 VVTALSARG-VIMAIRVTDLPIWGIQFHPESHITEHGLKILENFIK 190
                                           *******99.**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (192 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: 13.85
//
[ok]

This GapMind analysis is from Jul 25 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