GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Methanosarcina acetivorans C2A

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_011022929.1 MA_RS15675 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>NCBI__GCF_000007345.1:WP_011022929.1
          Length = 370

 Score =  255 bits (652), Expect = 1e-72
 Identities = 147/329 (44%), Positives = 204/329 (62%), Gaps = 8/329 (2%)

Query: 4   VKKAILGEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAA 63
           +KK   G  L  EEA   +  +++           L+AL  +GE+P EIA   R M++A 
Sbjct: 8   IKKLEEGSDLSSEEAEAAIGEILS-TAEDEEIGAFLLALRAKGEKPQEIAGFVRGMKQAG 66

Query: 64  RPLR-VHRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLL 122
             ++ V    ++D  GTGGDG   +N+ST AA+V AA GV VAKHGNRAA+S +GS+D+L
Sbjct: 67  NTIKPVTPFRVIDTCGTGGDGLNTINVSTAAAIVTAAAGVPVAKHGNRAATSMSGSSDVL 126

Query: 123 EALGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNP 182
           EALG+ ++  P +V + IE++G GF+FA VFHPAM+ VA VR +LGVRTVFN+LGPLTNP
Sbjct: 127 EALGIKVDLTPGQVRKTIEKIGIGFMFAPVFHPAMKRVAGVRKKLGVRTVFNILGPLTNP 186

Query: 183 AGADAYVLGVFSPEWLAPMAEALERLGA-RGLVVHGEGADELV-LGENRVVEVGKG---A 237
           AGA   V+GVF  +   P+A AL  LG    LVVHG+G DE+   GE  V E+  G    
Sbjct: 187 AGAKGQVVGVFDKKLCEPIAYALAELGTEHALVVHGDGMDEISNTGETFVAELKDGEVST 246

Query: 238 YALTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKT 297
           Y +TPE +G+ RA  E +KGG P+ENA     + KG +KGP  D V L A A  Y +G  
Sbjct: 247 YTITPEAMGMLRAKPEDIKGGTPKENARDLLCIFKG-QKGPKRDLVILNAAAALYVSGIV 305

Query: 298 PSLKEGVALAREVLASGEAYLLLERYVAF 326
            S+++ + +A + + SG+  +   ++  F
Sbjct: 306 GSIRQAIPIAEDAIDSGKVMVKFNQFRNF 334


Lambda     K      H
   0.317    0.136    0.380 

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: 352
Number of extensions: 21
Number of successful extensions: 5
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: 329
Length of database: 370
Length adjustment: 29
Effective length of query: 300
Effective length of database: 341
Effective search space:   102300
Effective search space used:   102300
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_011022929.1 MA_RS15675 (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.1815993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-129  417.4   0.5   2.5e-129  417.2   0.5    1.0  1  NCBI__GCF_000007345.1:WP_011022929.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_011022929.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   0.5  2.5e-129  2.5e-129       1     328 [.       8     332 ..       8     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 2.5e-129
                             TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvD 73 
                                           ++kl ++ dLs+eeae+++ ei+s  a+d++i+A+l alr+kge+++eiag+++ +++  ++++  +  +++D
  NCBI__GCF_000007345.1:WP_011022929.1   8 IKKLEEGSDLSSEEAEAAIGEILST-AEDEEIGAFLLALRAKGEKPQEIAGFVRGMKQAGNTIKPVTPFRVID 79 
                                           578999******************7.***************************************99****** PP

                             TIGR01245  74 ivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFl 146
                                           ++GTGGDgl+tiN+STa+a+v aaaGv+vaKhGnr+++s sGs+DvLealg++++l+p +v++++e+ gigF+
  NCBI__GCF_000007345.1:WP_011022929.1  80 TCGTGGDGLNTINVSTAAAIVTAAAGVPVAKHGNRAATSMSGSSDVLEALGIKVDLTPGQVRKTIEKIGIGFM 152
                                           ************************************************************************* PP

                             TIGR01245 147 fAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedg 219
                                           fAP +hpa+k+va+vRk+LgvrtvfN+LGPL+nPa ak qv+Gv++k+l+e +a +l +lg+++alvvhg dg
  NCBI__GCF_000007345.1:WP_011022929.1 153 FAPVFHPAMKRVAGVRKKLGVRTVFNILGPLTNPAGAKGQVVGVFDKKLCEPIAYALAELGTEHALVVHG-DG 224
                                           **********************************************************************.** PP

                             TIGR01245 220 lDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaa 292
                                           +DEis tget vaelkdge+++yt++pe +g+ ra+ e++kgg+++ena++l  +++g++ ++krd+v+lNaa
  NCBI__GCF_000007345.1:WP_011022929.1 225 MDEISNTGETFVAELKDGEVSTYTITPEAMGMLRAKPEDIKGGTPKENARDLLCIFKGQK-GPKRDLVILNAA 296
                                           **********************************************************98.99********** PP

                             TIGR01245 293 aalyvagkakdlkegvelakeaiksgkalekleelv 328
                                           aalyv+g + ++++++  a++ai+sgk++ k++++ 
  NCBI__GCF_000007345.1:WP_011022929.1 297 AALYVSGIVGSIRQAIPIAEDAIDSGKVMVKFNQFR 332
                                           ****************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (370 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: 26.03
//
[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