Alignments for a candidate for dapE in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Herbaspirillum seropedicae SmR1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate HSERO_RS10790 HSERO_RS10790 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__HerbieS:HSERO_RS10790
          Length = 375

 Score =  477 bits (1227), Expect = e-139
 Identities = 231/374 (61%), Positives = 281/374 (75%)

Query: 4   TQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVV 63
           +++L L +EL+S  SVTP+D+ CQ  LAE L  +GF  E +  G+  N+W R+GT  P+V
Sbjct: 2   SKTLALTQELMSLSSVTPEDKGCQARLAELLTPLGFVCETIQSGEVTNLWARKGTAQPLV 61

Query: 64  CFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNH 123
            FAGHTDVVPTGP+EKW S PF+P  R+GRLYGRGA+DMKTSIA  V ACE F A HP+H
Sbjct: 62  VFAGHTDVVPTGPLEKWQSHPFQPTLREGRLYGRGASDMKTSIAAMVVACEEFTAAHPDH 121

Query: 124 QGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSL 183
           +GSI  LITSDEEG A+DGT  V + LKAR E +DYCIVGEPT+   LGDMIKNGRRG++
Sbjct: 122 KGSIGFLITSDEEGPAIDGTVVVCNALKARGEQLDYCIVGEPTSAKTLGDMIKNGRRGTM 181

Query: 184 SGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTG 243
           SG LTVKG QGHIAYP LA NP+H  APAL EL  E WD GNEY+ PTS+QISNI+GGTG
Sbjct: 182 SGKLTVKGIQGHIAYPQLARNPIHQAAPALAELVAEQWDAGNEYYLPTSWQISNIHGGTG 241

Query: 244 ATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLT 303
           A+NVIPGE+ + FNFRFST ST  GL+QRVHAILDKHG++YDL+W+  G PFLT  G L+
Sbjct: 242 ASNVIPGEVMIDFNFRFSTASTVEGLQQRVHAILDKHGLEYDLKWTVGGLPFLTPRGDLS 301

Query: 304 DVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPK 363
           D    AI +  G++ ELSTTGGTSDGRFI  I  ++IE GP N +IH+I+E++ +  I  
Sbjct: 302 DALSKAIKDETGLDTELSTTGGTSDGRFIAQICPQVIEFGPPNDSIHKIDEHIEVRYIDP 361

Query: 364 LSAVYEGILARLLA 377
           L  +Y   L  LLA
Sbjct: 362 LKNIYRKTLENLLA 375


Lambda     K      H
   0.317    0.135    0.400 

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: 470
Number of extensions: 15
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: 381
Length of database: 375
Length adjustment: 30
Effective length of query: 351
Effective length of database: 345
Effective search space:   121095
Effective search space used:   121095
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate HSERO_RS10790 HSERO_RS10790 (succinyl-diaminopimelate desuccinylase)
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.18025.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-164  531.5   0.0   6.3e-164  531.3   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS10790  HSERO_RS10790 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS10790  HSERO_RS10790 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.3   0.0  6.3e-164  6.3e-164       3     370 .]       6     373 ..       4     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 531.3 bits;  conditional E-value: 6.3e-164
                                  TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaG 70 
                                                +l++eL+s+ svtP+d+g+q+ +ae L+ lgf +e+++ ++++nlwa++gt +p +vfaGhtDvvP+G
  lcl|FitnessBrowser__HerbieS:HSERO_RS10790   6 ALTQELMSLSSVTPEDKGCQARLAELLTPLGFVCETIQSGEVTNLWARKGTAQPLVVFAGHTDVVPTG 73 
                                                799***************************************************************** PP

                                  TIGR01246  71 elekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGt 138
                                                +lekW+s+pf+p+ r+G+lygrGa Dmk+s+aa+vva+e+f ++++dhkGs+++litsDeeg aidGt
  lcl|FitnessBrowser__HerbieS:HSERO_RS10790  74 PLEKWQSHPFQPTLREGRLYGRGASDMKTSIAAMVVACEEFTAAHPDHKGSIGFLITSDEEGPAIDGT 141
                                                ******************************************************************** PP

                                  TIGR01246 139 kkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavp 206
                                                + v + lk+r e++dy++vgeP+s+k+lGD+ik+GrrG ++gkl++kGiqGh+aYP++a+nP+h+a+p
  lcl|FitnessBrowser__HerbieS:HSERO_RS10790 142 VVVCNALKARGEQLDYCIVGEPTSAKTLGDMIKNGRRGTMSGKLTVKGIQGHIAYPQLARNPIHQAAP 209
                                                ******************************************************************** PP

                                  TIGR01246 207 vlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildk 274
                                                +l+el+a+++D Gne++ p+s qi+ni++gtgasnviPge+ + fn+rfs+ +++e l+++v++ildk
  lcl|FitnessBrowser__HerbieS:HSERO_RS10790 210 ALAELVAEQWDAGNEYYLPTSWQISNIHGGTGASNVIPGEVMIDFNFRFSTASTVEGLQQRVHAILDK 277
                                                ******************************************************************** PP

                                  TIGR01246 275 hkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvnd 342
                                                h+l+Y+l+w++ g pflt +g+l +++ +ai+  ++  +elst+GGtsD+rfia++  +v+e+G+ nd
  lcl|FitnessBrowser__HerbieS:HSERO_RS10790 278 HGLEYDLKWTVGGLPFLTPRGDLSDALSKAIKDETGLDTELSTTGGTSDGRFIAQICPQVIEFGPPND 345
                                                ******************************************************************** PP

                                  TIGR01246 343 tihkvneavkiedleklsevyeklleel 370
                                                +ihk++e++++  ++ l+++y+k+le+l
  lcl|FitnessBrowser__HerbieS:HSERO_RS10790 346 SIHKIDEHIEVRYIDPLKNIYRKTLENL 373
                                                *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (375 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: 10.35
//
[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