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.29095.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: 8.95
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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