Alignments for a candidate for dapE in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Sinorhizobium meliloti 1021

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate SMc01096 SMc01096 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__Smeli:SMc01096
          Length = 397

 Score =  286 bits (731), Expect = 9e-82
 Identities = 162/390 (41%), Positives = 219/390 (56%), Gaps = 19/390 (4%)

Query: 5   PVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFE-----DTTNFWARRGTQ 59
           PV  LA  LI   SVTPA+ G    +   L  +GF+++ +V +     D  N +AR G +
Sbjct: 6   PVSNLAA-LIRCPSVTPAEGGALAALEAMLAPVGFKVDRVVAKEPGTPDIENLYARTGGE 64

Query: 60  SPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAE 119
            P  +FAGHTDVVP G  + W  PPF   + +G ++GRGA DMKG +AC + AV R I +
Sbjct: 65  GPHLMFAGHTDVVPVGDEAAWSRPPFSAAIAEGEMYGRGAVDMKGGIACFVAAVARHIEK 124

Query: 120 HPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGR 179
           H   +GSI FLIT DEEGP INGTV+++E   AR E  D C+VGEP++   +GD++K GR
Sbjct: 125 HGAPKGSISFLITGDEEGPAINGTVKLLEWAAARGERWDACLVGEPTNPDCIGDMIKIGR 184

Query: 180 RGSITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQ 239
           RGS++G + V G QGH AYPHLA+NPV   L     L    +D+G   F P++ ++  + 
Sbjct: 185 RGSLSGRITVHGVQGHAAYPHLADNPVRSILQIAQALMDPPFDDGTENFQPSNLEVTTID 244

Query: 240 AGTGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLD-----------YDVKW 288
            G  A NVIP +    FN RF+   T E +   + + LD                Y++ W
Sbjct: 245 VGNTAVNVIPAKASAAFNIRFNDRWTAESLMAEIVARLDRAAAGSALRPGRAPARYEIVW 304

Query: 289 T-LSGQPFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNA 347
                  FLT    L+ ++  AVE V  + P L TTGGTSD RFI      VVE G V  
Sbjct: 305 NERPSHVFLTRNNALIDSLSGAVEAVTGRQPQLSTTGGTSDARFIKDY-CPVVEFGLVGK 363

Query: 348 TIHKVNECVRIADLEKLTDMYQKTLNHLLG 377
           T+H V+E V +ADLE LT +Y+  +    G
Sbjct: 364 TMHMVDERVALADLETLTGIYETFIARWFG 393


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: 457
Number of extensions: 31
Number of successful extensions: 4
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: 397
Length adjustment: 30
Effective length of query: 347
Effective length of database: 367
Effective search space:   127349
Effective search space used:   127349
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 SMc01096 SMc01096 (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.30252.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.1e-128  413.8   0.0   3.7e-128  413.6   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc01096  SMc01096 succinyl-diaminopimelat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01096  SMc01096 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.6   0.0  3.7e-128  3.7e-128       5     369 ..      10     390 ..       7     391 .. 0.96

  Alignments for each domain:
  == domain 1  score: 413.6 bits;  conditional E-value: 3.7e-128
                           TIGR01246   5 akeLisrksvtPndagaqeliaerLkklgfeieilefe.....dtknlwatrgteepvlvfaGhtDvvPaGelek 74 
                                         +  Li+ +svtP++ ga++ +++ L  +gf+++++  +     d++nl+a+ g e p+l+faGhtDvvP+G++ +
  lcl|FitnessBrowser__Smeli:SMc01096  10 LAALIRCPSVTPAEGGALAALEAMLAPVGFKVDRVVAKepgtpDIENLYARTGGEGPHLMFAGHTDVVPVGDEAA 84 
                                         5679****************************9987543444489****************************** PP

                           TIGR01246  75 WssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerd 149
                                         Ws +pf++++ +G +ygrGa+Dmkg++a+fv+a+ r+++k+   kGs+s+lit Deeg ai+Gt+k++e+  +r 
  lcl|FitnessBrowser__Smeli:SMc01096  85 WSRPPFSAAIAEGEMYGRGAVDMKGGIACFVAAVARHIEKHGAPKGSISFLITGDEEGPAINGTVKLLEWAAARG 159
                                         *************************************************************************** PP

                           TIGR01246 150 elidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffp 224
                                         e  d ++vgeP+  + +GD+ikiGrrGs++g+++++G+qGh aYPh+a+nPv +++++ ++l++  +D+G+e f+
  lcl|FitnessBrowser__Smeli:SMc01096 160 ERWDACLVGEPTNPDCIGDMIKIGRRGSLSGRITVHGVQGHAAYPHLADNPVRSILQIAQALMDPPFDDGTENFQ 234
                                         *************************************************************************** PP

                           TIGR01246 225 psslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh...........kldYelewkl.sg 287
                                         ps+l+++ i++g+ a nviP++++++fn+rf+  +++e+l  ++++ ld+               Ye+ w+   +
  lcl|FitnessBrowser__Smeli:SMc01096 235 PSNLEVTTIDVGNTAVNVIPAKASAAFNIRFNDRWTAESLMAEIVARLDRAaagsalrpgraPARYEIVWNErPS 309
                                         *************************************************9989999999888899*****85268 PP

                           TIGR01246 288 epfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsev 362
                                         + flt+++ li+++  a+e v++++p+lst+GGtsDarfi+++ + vve+Glv +t+h v+e+v ++dle l+ +
  lcl|FitnessBrowser__Smeli:SMc01096 310 HVFLTRNNALIDSLSGAVEAVTGRQPQLSTTGGTSDARFIKDY-CPVVEFGLVGKTMHMVDERVALADLETLTGI 383
                                         99*****************************************.******************************* PP

                           TIGR01246 363 yekllee 369
                                         ye+++++
  lcl|FitnessBrowser__Smeli:SMc01096 384 YETFIAR 390
                                         ***9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (397 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.11
//
[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