Alignments for a candidate for trpD_2 in Methanosarcina acetivorans C2A

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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

GapMind for Amino acid biosynthesis