Alignments for a candidate for dapE in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Shewanella loihica PV-4

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate 5209391 Shew_1862 succinyl-diaminopimelate desuccinylase (RefSeq)

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__PV4:5209391
          Length = 376

 Score =  530 bits (1364), Expect = e-155
 Identities = 254/371 (68%), Positives = 297/371 (80%)

Query: 6   VLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFVF 65
           VL LA++LI+R SVTP D GCQ LM +RL A GF IE MVFEDTTN WARRG Q PLF F
Sbjct: 5   VLTLAQDLIARASVTPLDEGCQPLMAKRLAAKGFNIEPMVFEDTTNMWARRGDQGPLFCF 64

Query: 66  AGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQG 125
           AGHTDVVP G L++WHTPPFEP VIDG+LHGRGAADMKGSLA M+VA ERF+ +HPDH+G
Sbjct: 65  AGHTDVVPVGDLNRWHTPPFEPVVIDGYLHGRGAADMKGSLAAMVVATERFVDKHPDHKG 124

Query: 126 SIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGSITG 185
           SI FLITSDEEGPFINGT RV++TL ARNE I   +VGEPSST  +GD+VKNGRRGS+TG
Sbjct: 125 SIAFLITSDEEGPFINGTTRVIDTLEARNEKITWSLVGEPSSTHKLGDIVKNGRRGSLTG 184

Query: 186 DLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGTGAS 245
           +L VKG QGHVAYPHLA+NP+HKA PAL ELA  +WD GN +FPPTSFQI N+  GTGAS
Sbjct: 185 NLTVKGVQGHVAYPHLADNPIHKAAPALDELARMKWDNGNEFFPPTSFQIANINGGTGAS 244

Query: 246 NVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGELLAA 305
           NVIPG  +V FNFR+STE+T E + +RV ++LDAHGLDYD+ W  +G PFLTD G LL A
Sbjct: 245 NVIPGSLEVMFNFRYSTEVTAEILIQRVLNILDAHGLDYDISWIFNGLPFLTDAGPLLDA 304

Query: 306 VVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKLT 365
              A+ E+        T+GGTSDGRFIA  GAQV+ELGPVNATIHKVNECV++ D+E+L 
Sbjct: 305 TREAIYEITGTETDPQTSGGTSDGRFIAPTGAQVIELGPVNATIHKVNECVKVEDIEQLA 364

Query: 366 DMYQKTLNHLL 376
            +Y++ L  LL
Sbjct: 365 KVYERILEKLL 375


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: 543
Number of extensions: 14
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: 377
Length of database: 376
Length adjustment: 30
Effective length of query: 347
Effective length of database: 346
Effective search space:   120062
Effective search space used:   120062
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 5209391 Shew_1862 (succinyl-diaminopimelate desuccinylase (RefSeq))
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.7574.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.5e-175  567.6   0.0   6.3e-175  567.5   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209391  Shew_1862 succinyl-diaminopimela


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209391  Shew_1862 succinyl-diaminopimelate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.5   0.0  6.3e-175  6.3e-175       2     370 .]       6     374 ..       5     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 567.5 bits;  conditional E-value: 6.3e-175
                        TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWssdp 79 
                                      l la++Li r svtP d+g+q l+a+rL + gf+ie + fedt+n+wa+rg + p ++faGhtDvvP+G+l++W+++p
  lcl|FitnessBrowser__PV4:5209391   6 LTLAQDLIARASVTPLDEGCQPLMAKRLAAKGFNIEPMVFEDTTNMWARRGDQGPLFCFAGHTDVVPVGDLNRWHTPP 83 
                                      679*************************************************************************** PP

                        TIGR01246  80 fepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidyavv 157
                                      fep+++dG+l+grGaaDmkgslaa+vva+erfv k++dhkGs+++litsDeeg +i+Gt++v++tl++r+e+i++++v
  lcl|FitnessBrowser__PV4:5209391  84 FEPVVIDGYLHGRGAADMKGSLAAMVVATERFVDKHPDHKGSIAFLITSDEEGPFINGTTRVIDTLEARNEKITWSLV 161
                                      ****************************************************************************** PP

                        TIGR01246 158 gePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqianiea 235
                                      gePss++klGD++k+GrrGs+tg+l++kG+qGhvaYPh+a+nP+hka+p+l el+ +k+D+Gneffpp+s+qiani++
  lcl|FitnessBrowser__PV4:5209391 162 GEPSSTHKLGDIVKNGRRGSLTGNLTVKGVQGHVAYPHLADNPIHKAAPALDELARMKWDNGNEFFPPTSFQIANING 239
                                      ****************************************************************************** PP

                        TIGR01246 236 gtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkp 313
                                      gtgasnviPg+l+v+fn+r+s+ev++e l ++v +ild+h+ldY++ w + g pflt++g l+++ +eai e++++++
  lcl|FitnessBrowser__PV4:5209391 240 GTGASNVIPGSLEVMFNFRYSTEVTAEILIQRVLNILDAHGLDYDISWIFNGLPFLTDAGPLLDATREAIYEITGTET 317
                                      ****************************************************************************** PP

                        TIGR01246 314 elstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                      + +tsGGtsD+rfia  ga+v+elG+vn+tihkvne+vk+ed+e+l++vye++le+l
  lcl|FitnessBrowser__PV4:5209391 318 DPQTSGGTSDGRFIAPTGAQVIELGPVNATIHKVNECVKVEDIEQLAKVYERILEKL 374
                                      ******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (376 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: 12.14
//
[ok]

This GapMind analysis is from Apr 09 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