Alignments for a candidate for dapE in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Shewanella amazonensis SB2B

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate 6937491 Sama_1647 succinyl-diaminopimelate desuccinylase (RefSeq)

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__SB2B:6937491
          Length = 382

 Score =  541 bits (1395), Expect = e-159
 Identities = 264/375 (70%), Positives = 301/375 (80%)

Query: 2   TDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSP 61
           T S V+ L +ELISR SVTP D GCQDLM +RL A+GF IE MVFEDTTN WARRGT+ P
Sbjct: 6   THSDVIELTRELISRPSVTPLDEGCQDLMAKRLAAIGFTIEPMVFEDTTNLWARRGTEGP 65

Query: 62  LFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHP 121
           +F FAGHTDVVP G L++WHTPPF+P VIDG++HGRGAADMKGSLA M+VA ERF+AEHP
Sbjct: 66  VFCFAGHTDVVPVGDLNRWHTPPFDPVVIDGYIHGRGAADMKGSLAAMVVAAERFVAEHP 125

Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181
           DHQGSI FLITSDEEGPFINGTVRVVETL AR+E I   +VGEPSST  +GDVVKNGRRG
Sbjct: 126 DHQGSIAFLITSDEEGPFINGTVRVVETLEARHEKITWALVGEPSSTHLLGDVVKNGRRG 185

Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241
           S+TG+L VKG QGHVAYPHLA+NP+H+A PALAEL+  +WD+GN +FPPTSFQI N+  G
Sbjct: 186 SLTGNLTVKGIQGHVAYPHLADNPIHRAAPALAELSRIEWDKGNEFFPPTSFQIANINGG 245

Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301
           TGASNVIPGE  V FNFR+STE+T E +  RV  +LDAHGLDYD+ W  +G PFLT  G 
Sbjct: 246 TGASNVIPGELKVMFNFRYSTEVTAETLIARVLGILDAHGLDYDIDWVFNGLPFLTGEGP 305

Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361
           LL A   A+ EV        TTGGTSDGRFIA  GAQV+ELGPVNATIHKVNECV+ +DL
Sbjct: 306 LLDATREAIFEVTGTHTDPQTTGGTSDGRFIAPTGAQVIELGPVNATIHKVNECVKASDL 365

Query: 362 EKLTDMYQKTLNHLL 376
           E LT  YQ+ L  LL
Sbjct: 366 ELLTGCYQRILEKLL 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: 570
Number of extensions: 12
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: 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 6937491 Sama_1647 (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.25442.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.9e-175  568.1   0.0   4.5e-175  568.0   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937491  Sama_1647 succinyl-diaminopimela


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937491  Sama_1647 succinyl-diaminopimelate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.0   0.0  4.5e-175  4.5e-175       2     370 .]      11     379 ..      10     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 568.0 bits;  conditional E-value: 4.5e-175
                         TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWssd 78 
                                       +el++eLisr+svtP d+g+q+l+a+rL ++gf+ie + fedt+nlwa+rgte pv++faGhtDvvP+G+l++W+++
  lcl|FitnessBrowser__SB2B:6937491  11 IELTRELISRPSVTPLDEGCQDLMAKRLAAIGFTIEPMVFEDTTNLWARRGTEGPVFCFAGHTDVVPVGDLNRWHTP 87 
                                       799************************************************************************** PP

                         TIGR01246  79 pfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidya 155
                                       pf+p+++dG+++grGaaDmkgslaa+vvaaerfv++++dh+Gs+++litsDeeg +i+Gt++vvetl++r+e+i++a
  lcl|FitnessBrowser__SB2B:6937491  88 PFDPVVIDGYIHGRGAADMKGSLAAMVVAAERFVAEHPDHQGSIAFLITSDEEGPFINGTVRVVETLEARHEKITWA 164
                                       ***************************************************************************** PP

                         TIGR01246 156 vvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqian 232
                                       +vgePss++ lGDv+k+GrrGs+tg+l++kGiqGhvaYPh+a+nP+h+a+p+l+el  i++D+Gneffpp+s+qian
  lcl|FitnessBrowser__SB2B:6937491 165 LVGEPSSTHLLGDVVKNGRRGSLTGNLTVKGIQGHVAYPHLADNPIHRAAPALAELSRIEWDKGNEFFPPTSFQIAN 241
                                       ***************************************************************************** PP

                         TIGR01246 233 ieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevl 309
                                       i++gtgasnviPgelkv+fn+r+s+ev++e+l  +v  ild+h+ldY+++w + g pflt eg l+++ +eai ev+
  lcl|FitnessBrowser__SB2B:6937491 242 INGGTGASNVIPGELKVMFNFRYSTEVTAETLIARVLGILDAHGLDYDIDWVFNGLPFLTGEGPLLDATREAIFEVT 318
                                       ***************************************************************************** PP

                         TIGR01246 310 kkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                       +++++ +t+GGtsD+rfia  ga+v+elG+vn+tihkvne+vk +dle l+  y+++le+l
  lcl|FitnessBrowser__SB2B:6937491 319 GTHTDPQTTGGTSDGRFIAPTGAQVIELGPVNATIHKVNECVKASDLELLTGCYQRILEKL 379
                                       **********************************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.74
//
[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