Alignments for a candidate for trpD_1 in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_1 in Shewanella amazonensis SB2B

Align Aminodeoxychorismate/anthranilate synthase component 2; ADC synthase; ADCS; 4-amino-4-deoxychorismate synthase component 2; Aminodeoxychorismate synthase, glutamine amidotransferase component; EC 2.6.1.85; EC 4.1.3.27 (characterized)
to candidate 6938912 Sama_3015 para-aminobenzoate synthase glutamine amidotransferase, component II (RefSeq)

Query= SwissProt::P28819
         (194 letters)



>FitnessBrowser__SB2B:6938912
          Length = 216

 Score =  244 bits (623), Expect = 8e-70
 Identities = 118/190 (62%), Positives = 151/190 (79%), Gaps = 6/190 (3%)

Query: 1   MILMIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAG 60
           M+LMIDNYDSFT+NLVQY  +LGEE+VV+R+D IT++EI  L+PD+L+ISPGPC+PD+AG
Sbjct: 26  MLLMIDNYDSFTFNLVQYFQQLGEEVVVRRHDDITLEEIAALAPDYLVISPGPCTPDDAG 85

Query: 61  ISLEAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKN 120
           +SL+AI HFAGK+PI GVCLGHQ++AQVFG  V+RA R+MHGKTSDI H+ + +F GL N
Sbjct: 86  VSLDAITHFAGKLPILGVCLGHQAMAQVFGAKVIRAGRVMHGKTSDISHNNQRLFRGLNN 145

Query: 121 PLVATRYHSLIVKPETLPSCFTVTAQTKE----GEIMAIRHNDLPIEGVQFHPESIMTSF 176
           PL  TRYHSL+V  E++P  F + A   +     EIMAI H  LP+ GVQFHPESI+T  
Sbjct: 146 PLRVTRYHSLLV--ESVPEGFVMDAWFDDPVHGREIMAISHKSLPLYGVQFHPESILTEQ 203

Query: 177 GKEMLRNFIE 186
           G E+L NF++
Sbjct: 204 GLELLGNFLK 213


Lambda     K      H
   0.320    0.139    0.404 

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: 171
Number of extensions: 4
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: 194
Length of database: 216
Length adjustment: 21
Effective length of query: 173
Effective length of database: 195
Effective search space:    33735
Effective search space used:    33735
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: 45 (21.9 bits)

Align candidate 6938912 Sama_3015 (para-aminobenzoate synthase glutamine amidotransferase, component II (RefSeq))
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)

# 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/TIGR00566.hmm
# target sequence database:        /tmp/gapView.30192.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00566  [M=192]
Accession:   TIGR00566
Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.5e-84  267.4   0.0      4e-84  267.2   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6938912  Sama_3015 para-aminobenzoate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938912  Sama_3015 para-aminobenzoate synthase glutamine amidotransferase, component II (Ref
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.2   0.0     4e-84     4e-84       1     191 [.      26     213 ..      26     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 267.2 bits;  conditional E-value: 4e-84
                         TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPi 77 
                                       m+l+idnydsft+nlvq++++lg+evvv+r d++tl+ei al+p+  +visPGPctPd+a++s l++i h+aGklPi
  lcl|FitnessBrowser__SB2B:6938912  26 MLLMIDNYDSFTFNLVQYFQQLGEEVVVRRHDDITLEEIAALAPDY-LVISPGPCTPDDAGVS-LDAITHFAGKLPI 100
                                       79********************************************.****************.************* PP

                         TIGR00566  78 lGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeee 154
                                       lGvClGhqa+aq+fGa+v+ra +v+hGk+s+i+hn++ +f+gl nP  l++tryhsl ve  ++++ + + a+ + +
  lcl|FitnessBrowser__SB2B:6938912 101 LGVCLGHQAMAQVFGAKVIRAGRVMHGKTSDISHNNQRLFRGLNNP--LRVTRYHSLLVE--SVPEGFVMDAWFDDP 173
                                       **********************************************..**********96..699999999998877 PP

                         TIGR00566 155 ...ieimairhrdlpleGvqfhPesilselGkellanflk 191
                                           eimai h+ lpl GvqfhPesil+e+G ell nflk
  lcl|FitnessBrowser__SB2B:6938912 174 vhgREIMAISHKSLPLYGVQFHPESILTEQGLELLGNFLK 213
                                       7789**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (216 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: 6.97
//
[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