Alignments for a candidate for trpD_2 in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Acidovorax sp. GW101-3H11

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate Ac3H11_771 Anthranilate phosphoribosyltransferase (EC 2.4.2.18)

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_771
          Length = 346

 Score =  470 bits (1209), Expect = e-137
 Identities = 235/338 (69%), Positives = 277/338 (81%)

Query: 1   MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60
           MPITPQ+ALQRTIEHREIFHDEM+ LMR IM+GE+S  M +AI+TGLRVKKETIGEI  A
Sbjct: 1   MPITPQEALQRTIEHREIFHDEMLHLMRLIMKGELSPLMTAAIITGLRVKKETIGEITAA 60

Query: 61  ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120
           A VMREFS +V V D +H+VDIVGTGGDG++TFNISTC+MFVAAA GAKV+KHG R VSS
Sbjct: 61  AQVMREFSTKVHVPDSKHLVDIVGTGGDGANTFNISTCSMFVAAAAGAKVSKHGGRGVSS 120

Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180
           KSGSAD +EALG  I L+PE +A  +A+ GIGFM+AP HHPAMK VAPVR+E+GVRTIFN
Sbjct: 121 KSGSADVMEALGIHINLKPESIAQCIAEVGIGFMFAPNHHPAMKNVAPVRKELGVRTIFN 180

Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240
           ILGPLTNPA +PNILMGVFHPDLVGIQ R LQ LGAE A+VV+GRDGMDE+SLGA TLVG
Sbjct: 181 ILGPLTNPASAPNILMGVFHPDLVGIQVRALQRLGAEHAMVVYGRDGMDEVSLGAATLVG 240

Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300
           EL++GQ+ EYE+HPEDFG++M+++R LKV    +SR ML+ VL   PG A DIV LNAG 
Sbjct: 241 ELKNGQITEYEIHPEDFGLSMASNRALKVETPEQSREMLIGVLKGEPGAAQDIVCLNAGV 300

Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338
           ALY A V DS+  G+ +AR  +A G+A A L+  V  T
Sbjct: 301 ALYAANVVDSVPAGLAKARAAIASGAALAKLEQMVTRT 338


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: 429
Number of extensions: 8
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: 345
Length of database: 346
Length adjustment: 29
Effective length of query: 316
Effective length of database: 317
Effective search space:   100172
Effective search space used:   100172
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 Ac3H11_771 (Anthranilate phosphoribosyltransferase (EC 2.4.2.18))
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.2645.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.1e-129  417.5   2.6   2.4e-129  417.3   2.6    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771  Anthranilate phosphoribosyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771  Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.3   2.6  2.4e-129  2.4e-129       1     328 [.       9     335 ..       9     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 417.3 bits;  conditional E-value: 2.4e-129
                                       TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkv 63 
                                                     l++ ++++++ ++e+ +lm+ im+ge+s+   aAi++ lrvk et+ ei+++a+++re ++kv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771   9 LQRTIEHREIFHDEMLHLMRLIMKGELSPLMTAAIITGLRVKKETIGEITAAAQVMREFSTKV 71 
                                                     578999********************************************************* PP

                                       TIGR01245  64 ekeeseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvn 126
                                                     ++ +s++lvDivGTGGDg++t+NiST s++vaaaaG+kv KhG r vssksGsaDv+ealg++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771  72 HVPDSKHLVDIVGTGGDGANTFNISTCSMFVAAAAGAKVSKHGGRGVSSKSGSADVMEALGIH 134
                                                     **9************************************************************ PP

                                       TIGR01245 127 lelspekvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlG 189
                                                     ++l+pe++a++++evgigF+fAP++hpa+k+vapvRkeLgvrt+fN+LGPL+nPa+a++ ++G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771 135 INLKPESIAQCIAEVGIGFMFAPNHHPAMKNVAPVRKELGVRTIFNILGPLTNPASAPNILMG 197
                                                     *************************************************************** PP

                                       TIGR01245 190 vyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglk 252
                                                     v+++dlv + +++l++lg+++a+vv g+dg+DE+sl + t v elk+g+i+ey+++pedfgl 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771 198 VFHPDLVGIQVRALQRLGAEHAMVVYGRDGMDEVSLGAATLVGELKNGQITEYEIHPEDFGLS 260
                                                     *************************************************************** PP

                                       TIGR01245 253 raeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeai 315
                                                     +a+ ++lk++++e++ e+l  vl+g+  +a++div lNa++aly+a++++++ +g+  a++ai
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771 261 MASNRALKVETPEQSREMLIGVLKGEP-GAAQDIVCLNAGVALYAANVVDSVPAGLAKARAAI 322
                                                     *************************99.899******************************** PP

                                       TIGR01245 316 ksgkalekleelv 328
                                                      sg+al+kle++v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_771 323 ASGAALAKLEQMV 335
                                                     **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (346 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.22
//
[ok]

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