Alignments for a candidate for trpD_2 in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Pedobacter sp. GW460-11-11-14-LB5

Align anthranilate phosphoribosyltransferase (EC 2.4.2.18) (characterized)
to candidate CA265_RS05010 CA265_RS05010 anthranilate phosphoribosyltransferase

Query= reanno::Pedo557:CA265_RS05010
         (329 letters)



>FitnessBrowser__Pedo557:CA265_RS05010
          Length = 329

 Score =  656 bits (1693), Expect = 0.0
 Identities = 329/329 (100%), Positives = 329/329 (100%)

Query: 1   MKKILNHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAM 60
           MKKILNHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAM
Sbjct: 1   MKKILNHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAM 60

Query: 61  LDMCVKVNLSGYDLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSS 120
           LDMCVKVNLSGYDLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSS
Sbjct: 61  LDMCVKVNLSGYDLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSS 120

Query: 121 NVMEYLGYTFTNNEDTLKRNLDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPM 180
           NVMEYLGYTFTNNEDTLKRNLDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPM
Sbjct: 121 NVMEYLGYTFTNNEDTLKRNLDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPM 180

Query: 181 VNPGQPKYQMVGVFSLELARLYAYLYQDTDKSYTIVHALEGYDEVSLTCDVKTFSNKGEQ 240
           VNPGQPKYQMVGVFSLELARLYAYLYQDTDKSYTIVHALEGYDEVSLTCDVKTFSNKGEQ
Sbjct: 181 VNPGQPKYQMVGVFSLELARLYAYLYQDTDKSYTIVHALEGYDEVSLTCDVKTFSNKGEQ 240

Query: 241 ILTLQDMGFDKVEVNAIKGGDTVESSAKIFMDVLNGKATDVQNNVVLCNSALAIKTIKPQ 300
           ILTLQDMGFDKVEVNAIKGGDTVESSAKIFMDVLNGKATDVQNNVVLCNSALAIKTIKPQ
Sbjct: 241 ILTLQDMGFDKVEVNAIKGGDTVESSAKIFMDVLNGKATDVQNNVVLCNSALAIKTIKPQ 300

Query: 301 QSFADCFYEAEESLMSKKALNSFKQLLAC 329
           QSFADCFYEAEESLMSKKALNSFKQLLAC
Sbjct: 301 QSFADCFYEAEESLMSKKALNSFKQLLAC 329


Lambda     K      H
   0.319    0.134    0.385 

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: 525
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: 329
Length of database: 329
Length adjustment: 28
Effective length of query: 301
Effective length of database: 301
Effective search space:    90601
Effective search space used:    90601
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 CA265_RS05010 CA265_RS05010 (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.16031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    4.2e-93  298.2   0.1    4.8e-93  298.0   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS05010  CA265_RS05010 anthranilate phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS05010  CA265_RS05010 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.0   0.1   4.8e-93   4.8e-93       2     328 ..       6     327 ..       5     329 .] 0.96

  Alignments for each domain:
  == domain 1  score: 298.0 bits;  conditional E-value: 4.8e-93
                                  TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 
                                                ++l++nk+ s+eea++++  i +g ++ +qiaA+++a +++  t++e++g+  a+++  +kv+  + +
  lcl|FitnessBrowser__Pedo557:CA265_RS05010   6 NHLFENKSFSREEAKNILISISEGAFNSSQIAAFITAYAMRNITVQELQGFRDAMLDMCVKVNL-SGY 72 
                                                7899**********************************************************99.5** PP

                                  TIGR01245  70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvars 137
                                                +l+D +GTGGDg +t+NiST s++v+a+aG +vaKhGn  vss +Gs++v+e lg+++ ++ + ++r 
  lcl|FitnessBrowser__Pedo557:CA265_RS05010  73 DLIDLCGTGGDGKDTFNISTLSSFVVAGAGHHVAKHGNYGVSSGCGSSNVMEYLGYTFTNNEDTLKRN 140
                                                ******************************************************************** PP

                                  TIGR01245 138 leevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlkn 205
                                                l+  gi+Fl+AP + pa+k vap+RkeLgv+t fN+LGP++nP ++k+q++Gv+s +l++++a   + 
  lcl|FitnessBrowser__Pedo557:CA265_RS05010 141 LDAAGICFLHAPLFNPAMKIVAPIRKELGVKTFFNMLGPMVNPGQPKYQMVGVFSLELARLYAYLYQD 208
                                                ***************************************************************99999 PP

                                  TIGR01245 206 lgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsa.eenaellk 272
                                                   +  ++vh+ +g DE+slt + k  + k ++i    l+ +d+g+++ e++++kgg++ e +a++++
  lcl|FitnessBrowser__Pedo557:CA265_RS05010 209 TDKS-YTIVHALEGYDEVSLTCDVKTFSNKGEQI----LTLQDMGFDKVEVNAIKGGDTvESSAKIFM 271
                                                8877.8999***********98877777776555....6668****************96678999** PP

                                  TIGR01245 273 evlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                                +vl+gk+++ ++++v+ N a a+++ + ++++++ +  a+e+++s+kal+ +++l 
  lcl|FitnessBrowser__Pedo557:CA265_RS05010 272 DVLNGKATDVQNNVVLCNSALAIKTIKPQQSFADCFYEAEESLMSKKALNSFKQLL 327
                                                **************************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (329 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.49
//
[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