Alignments for a candidate for dapE in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Pseudomonas stutzeri RCH2

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate GFF1581 Psest_1618 succinyl-diaminopimelate desuccinylase, proteobacterial clade

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__psRCH2:GFF1581
          Length = 382

 Score =  480 bits (1236), Expect = e-140
 Identities = 240/374 (64%), Positives = 279/374 (74%), Gaps = 1/374 (0%)

Query: 4   SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLF 63
           SP L LA ELI+R SVTP D GCQ LM +RL A GF IE M  ED  NFWA RG++ P+ 
Sbjct: 7   SPTLELACELINRPSVTPLDEGCQQLMTQRLAACGFAIEPMHIEDVENFWAIRGSEGPVL 66

Query: 64  VFAGHTDVVPAGPLSQWHTPPFEPTVID-GFLHGRGAADMKGSLACMIVAVERFIAEHPD 122
            FAGHTDVVP GPL  W  PPF   + + G LHGRGAADMKGSLA M+VAVERF A HPD
Sbjct: 67  CFAGHTDVVPTGPLQAWQNPPFSARIDEQGMLHGRGAADMKGSLAAMVVAVERFTAAHPD 126

Query: 123 HQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGS 182
           H+G I FLITSDEEGP  +GT  VVE L  R + +D CIVGEPSST  VGDVVKNGRRGS
Sbjct: 127 HKGQIAFLITSDEEGPAHHGTKAVVERLRERGQRLDWCIVGEPSSTTLVGDVVKNGRRGS 186

Query: 183 ITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGT 242
           + G L V+G QGHVAYPHLA NP+H A PALAELAA  WD+GNA+FPPTSFQI NL AGT
Sbjct: 187 LGGTLTVRGQQGHVAYPHLAKNPIHLAAPALAELAAEHWDDGNAFFPPTSFQISNLNAGT 246

Query: 243 GASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGEL 302
           G +NVIPG  +  FNFRFSTE T E++K+R  ++LD HGLD++V+W LSG PFLT+ G L
Sbjct: 247 GTTNVIPGTLEAVFNFRFSTESTVEQLKQRTAAILDKHGLDWNVEWALSGLPFLTEPGAL 306

Query: 303 LAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLE 362
           L  V  A+  V  +     T+GGTSDGRFIA +G QVVELGPVNATIH+V+E +  +DL+
Sbjct: 307 LDGVAKAIRSVTGRETTPSTSGGTSDGRFIATLGTQVVELGPVNATIHQVDEHILASDLD 366

Query: 363 KLTDMYQKTLNHLL 376
            LTD+Y  TL +LL
Sbjct: 367 LLTDIYYLTLVNLL 380


Lambda     K      H
   0.318    0.135    0.403 

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: 535
Number of extensions: 18
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: 377
Length of database: 382
Length adjustment: 30
Effective length of query: 347
Effective length of database: 352
Effective search space:   122144
Effective search space used:   122144
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1581 Psest_1618 (succinyl-diaminopimelate desuccinylase, proteobacterial clade)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

# 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/TIGR01246.hmm
# target sequence database:        /tmp/gapView.20485.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01246  [M=370]
Accession:   TIGR01246
Description: dapE_proteo: succinyl-diaminopimelate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-167  543.6   0.0   1.3e-167  543.4   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1581  Psest_1618 succinyl-diaminopimel


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1581  Psest_1618 succinyl-diaminopimelate desuccinylase, proteobacterial clade
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.4   0.0  1.3e-167  1.3e-167       2     370 .]      10     379 ..       9     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 543.4 bits;  conditional E-value: 1.3e-167
                           TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWs 76 
                                         lela+eLi+r+svtP d+g+q+l+++rL + gf+ie +++ed++n+wa rg e pvl+faGhtDvvP+G+l++W+
  lcl|FitnessBrowser__psRCH2:GFF1581  10 LELACELINRPSVTPLDEGCQQLMTQRLAACGFAIEPMHIEDVENFWAIRGSEGPVLCFAGHTDVVPTGPLQAWQ 84 
                                         689************************************************************************ PP

                           TIGR01246  77 sdpfepee.rdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerde 150
                                         ++pf++++ ++G+l+grGaaDmkgslaa+vva+erf ++++dhkG++++litsDeeg a +Gtk+vve l+er +
  lcl|FitnessBrowser__psRCH2:GFF1581  85 NPPFSARIdEQGMLHGRGAADMKGSLAAMVVAVERFTAAHPDHKGQIAFLITSDEEGPAHHGTKAVVERLRERGQ 159
                                         *****987257**************************************************************** PP

                           TIGR01246 151 lidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffpp 225
                                          +d+++vgePss+  +GDv+k+GrrGs+ g+l+++G qGhvaYPh+a+nP+h a+p+l+el+a+++D+Gn+ffpp
  lcl|FitnessBrowser__psRCH2:GFF1581 160 RLDWCIVGEPSSTTLVGDVVKNGRRGSLGGTLTVRGQQGHVAYPHLAKNPIHLAAPALAELAAEHWDDGNAFFPP 234
                                         *************************************************************************** PP

                           TIGR01246 226 sslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikk 300
                                         +s+qi+n++agtg++nviPg l++ fn+rfs+e+++e+lk++ ++ildkh+ld+++ew lsg pflt+ g l++ 
  lcl|FitnessBrowser__psRCH2:GFF1581 235 TSFQISNLNAGTGTTNVIPGTLEAVFNFRFSTESTVEQLKQRTAAILDKHGLDWNVEWALSGLPFLTEPGALLDG 309
                                         *************************************************************************** PP

                           TIGR01246 301 vaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                         va+ai+ v++++++ stsGGtsD+rfia+lg++vvelG+vn+tih+v+e++  +dl+ l+++y+ +l +l
  lcl|FitnessBrowser__psRCH2:GFF1581 310 VAKAIRSVTGRETTPSTSGGTSDGRFIATLGTQVVELGPVNATIHQVDEHILASDLDLLTDIYYLTLVNL 379
                                         ****************************************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (382 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: 00:00:00.01
# Mc/sec: 11.95
//
[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