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

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.13690.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: 00:00:00.01
# Mc/sec: 10.69
//
[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