Alignments for a candidate for trpD_2 in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Methylococcus capsulatus Bath

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_010961801.1 MCA_RS12670 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_000008325.1:WP_010961801.1
          Length = 341

 Score =  319 bits (817), Expect = 7e-92
 Identities = 173/337 (51%), Positives = 223/337 (66%), Gaps = 1/337 (0%)

Query: 7   QALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMRE 66
           + L+  +  +++    M + MR+IM G  + A + A L  LR K ET+ E+A AA V+RE
Sbjct: 5   EVLETLLAGKDLSPSAMRETMRKIMSGGATPAQIGAFLIALRCKGETVEEVAAAAQVLRE 64

Query: 67  FSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSAD 126
            + +V V+   H++D  GTGGD S TFNIST A FV AA G +VAKHG+RSVS +SGSAD
Sbjct: 65  MATKVPVS-APHLLDTCGTGGDASKTFNISTTAAFVVAAAGGRVAKHGSRSVSGRSGSAD 123

Query: 127 ALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLT 186
            LEA G  IEL P+QV   +   G+GF++A  HH AMK     RRE+GVRT+FN+LGPLT
Sbjct: 124 VLEAAGINIELTPDQVKTCIETLGVGFLFAQRHHGAMKYAIGPRRELGVRTLFNLLGPLT 183

Query: 187 NPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQ 246
           NPAG+PN L+GV+    V   ARVLQ+LG+   LVV   DG+DE+S+ A T V EL++G 
Sbjct: 184 NPAGAPNQLVGVYTDPWVEGLARVLQQLGSSHVLVVHAEDGLDEISIAAPTHVAELKNGL 243

Query: 247 VHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYVAG 306
           +  Y V PE FG   +A   L +   A S  M+  VLDNVPGPA DIVALNAGAA+Y A 
Sbjct: 244 ITNYYVRPEQFGFRRAALSELAIDTVAASLKMMRGVLDNVPGPARDIVALNAGAAIYAAD 303

Query: 307 VADSIADGIVRARQVLADGSARACLDAYVAFTQQATA 343
           + DS+  GI RA  V+ADGSARA L+A  A ++Q  A
Sbjct: 304 LTDSLEAGIRRAEAVIADGSARAKLEALAALSRQFAA 340


Lambda     K      H
   0.320    0.134    0.377 

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: 319
Number of extensions: 10
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: 345
Length of database: 341
Length adjustment: 29
Effective length of query: 316
Effective length of database: 312
Effective search space:    98592
Effective search space used:    98592
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_010961801.1 MCA_RS12670 (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.19673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-125  404.6   0.4     2e-125  404.4   0.4    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010961801.1  MCA_RS12670 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010961801.1  MCA_RS12670 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.4   0.4    2e-125    2e-125       1     329 [.       7     333 ..       7     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 404.4 bits;  conditional E-value: 2e-125
                                 TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                               le+ll +kdLs   +++ m++imsg a++aqi+A+l+alr kget+ee+a++a++lre a+kv+++ + 
  lcl|NCBI__GCF_000008325.1:WP_010961801.1   7 LETLLAGKDLSPSAMRETMRKIMSGGATPAQIGAFLIALRCKGETVEEVAAAAQVLREMATKVPVS-AP 74 
                                               57899************************************************************5.9* PP

                                 TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138
                                               +l+D++GTGGD++kt+NiST++a+v+aaaG +vaKhG+rsvs++sGsaDvLea g+n+el+p++v+ ++
  lcl|NCBI__GCF_000008325.1:WP_010961801.1  75 HLLDTCGTGGDASKTFNISTTAAFVVAAAGGRVAKHGSRSVSGRSGSADVLEAAGINIELTPDQVKTCI 143
                                               ********************************************************************* PP

                                 TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207
                                               e++g+gFlfA ++h a+k++++ R+eLgvrt+fNlLGPL+nPa a++q++Gvy    ve la+vl++lg
  lcl|NCBI__GCF_000008325.1:WP_010961801.1 144 ETLGVGFLFAQRHHGAMKYAIGPRRELGVRTLFNLLGPLTNPAGAPNQLVGVYTDPWVEGLARVLQQLG 212
                                               ********************************************************************* PP

                                 TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276
                                               ++++lvvh+edglDEis+ ++t+vaelk+g i++y+++pe+fg+ ra l+el++++ ++++++++ vl 
  lcl|NCBI__GCF_000008325.1:WP_010961801.1 213 SSHVLVVHAEDGLDEISIAAPTHVAELKNGLITNYYVRPEQFGFRRAALSELAIDTVAASLKMMRGVLD 281
                                               ********************************************************************9 PP

                                 TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                               +   +++rdiv+lNa+aa+y+a+ +++l++g+++a+++i +g+a +kle+l+a
  lcl|NCBI__GCF_000008325.1:WP_010961801.1 282 NVP-GPARDIVALNAGAAIYAADLTDSLEAGIRRAEAVIADGSARAKLEALAA 333
                                               988.999*****************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (341 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.76
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 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 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