GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Shewanella sp. ANA-3

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate 7024734 Shewana3_1912 succinyl-diaminopimelate desuccinylase (RefSeq)

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__ANA3:7024734
          Length = 381

 Score =  522 bits (1344), Expect = e-153
 Identities = 255/372 (68%), Positives = 293/372 (78%)

Query: 5   PVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFV 64
           PV  L KELI+R SVTP D GCQ LM ERL A+GF IE MVFEDTTN WARRG + P+F 
Sbjct: 9   PVTELTKELIARPSVTPLDEGCQTLMAERLAAIGFNIEPMVFEDTTNMWARRGNEGPVFC 68

Query: 65  FAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQ 124
           FAGHTDVVPAG LS+WHTPPFEPT+IDG+L+GRGAADMKGSLA MIVA ERF+A+HP+H 
Sbjct: 69  FAGHTDVVPAGDLSRWHTPPFEPTIIDGYLYGRGAADMKGSLAAMIVATERFVAKHPNHP 128

Query: 125 GSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGSIT 184
           GSI FLITSDEEGPFINGT RV++TL ARNE I   +VGEPSSTL +GDVVKNGRRGS+T
Sbjct: 129 GSIAFLITSDEEGPFINGTTRVIDTLEARNEKITWTLVGEPSSTLKLGDVVKNGRRGSLT 188

Query: 185 GDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGTGA 244
            +L VKG QGHVAYPHLA+NP+HKA P LAEL+ T WD GN +FPPTS QI N+  GTGA
Sbjct: 189 ANLTVKGIQGHVAYPHLADNPIHKAAPFLAELSQTHWDNGNEFFPPTSMQIANINGGTGA 248

Query: 245 SNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGELLA 304
           SNVIPG  +V FNFR+STE+T E +  RV ++L AH LDYD+ WT +G PFLT  G LL 
Sbjct: 249 SNVIPGTLEVMFNFRYSTEVTAEILIERVEALLTAHELDYDISWTFNGLPFLTGEGPLLD 308

Query: 305 AVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKL 364
           A   A+ ++        TTGGTSDGRFIA  GA+V+ELGPVNATIHKVNECV+I DLE+L
Sbjct: 309 ATRHAIRQITGYDTDPQTTGGTSDGRFIAPTGAKVLELGPVNATIHKVNECVKIDDLEQL 368

Query: 365 TDMYQKTLNHLL 376
              Y+  L  LL
Sbjct: 369 ALCYEVILEQLL 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: 506
Number of extensions: 13
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: 381
Length adjustment: 30
Effective length of query: 347
Effective length of database: 351
Effective search space:   121797
Effective search space used:   121797
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 7024734 Shewana3_1912 (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.2371045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.3e-174  565.1   0.0   3.7e-174  564.9   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7024734  Shewana3_1912 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024734  Shewana3_1912 succinyl-diaminopimelate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.9   0.0  3.7e-174  3.7e-174       1     370 []      10     379 ..      10     379 .. 1.00

  Alignments for each domain:
  == domain 1  score: 564.9 bits;  conditional E-value: 3.7e-174
                         TIGR01246   1 vlelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWss 77 
                                       v+el+keLi r+svtP d+g+q l+aerL ++gf+ie + fedt+n+wa+rg e pv++faGhtDvvPaG+l++W++
  lcl|FitnessBrowser__ANA3:7024734  10 VTELTKELIARPSVTPLDEGCQTLMAERLAAIGFNIEPMVFEDTTNMWARRGNEGPVFCFAGHTDVVPAGDLSRWHT 86 
                                       589************************************************************************** PP

                         TIGR01246  78 dpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidy 154
                                       +pfep+++dG+lygrGaaDmkgslaa++va+erfv+k+++h Gs+++litsDeeg +i+Gt++v++tl++r+e+i++
  lcl|FitnessBrowser__ANA3:7024734  87 PPFEPTIIDGYLYGRGAADMKGSLAAMIVATERFVAKHPNHPGSIAFLITSDEEGPFINGTTRVIDTLEARNEKITW 163
                                       ***************************************************************************** PP

                         TIGR01246 155 avvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqia 231
                                       ++vgePss+ klGDv+k+GrrGs+t++l++kGiqGhvaYPh+a+nP+hka+p+l+el ++++D+Gneffpp+s+qia
  lcl|FitnessBrowser__ANA3:7024734 164 TLVGEPSSTLKLGDVVKNGRRGSLTANLTVKGIQGHVAYPHLADNPIHKAAPFLAELSQTHWDNGNEFFPPTSMQIA 240
                                       ***************************************************************************** PP

                         TIGR01246 232 nieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieev 308
                                       ni++gtgasnviPg l+v+fn+r+s+ev++e l ++ve++l +h+ldY++ w++ g pflt eg l+++ ++ai+++
  lcl|FitnessBrowser__ANA3:7024734 241 NINGGTGASNVIPGTLEVMFNFRYSTEVTAEILIERVEALLTAHELDYDISWTFNGLPFLTGEGPLLDATRHAIRQI 317
                                       ***************************************************************************** PP

                         TIGR01246 309 lkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                       ++  ++ +t+GGtsD+rfia  ga+v+elG+vn+tihkvne+vki+dle+l+  ye +le+l
  lcl|FitnessBrowser__ANA3:7024734 318 TGYDTDPQTTGGTSDGRFIAPTGAKVLELGPVNATIHKVNECVKIDDLEQLALCYEVILEQL 379
                                       **********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (381 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: 00:00:00.00
# Mc/sec: 18.31
//
[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