Alignments for a candidate for dapE in Rhizobium etli CFN 42

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Rhizobium etli CFN 42

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_042117802.1 RHE_RS02115 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>NCBI__GCF_000092045.1:WP_042117802.1
          Length = 397

 Score =  278 bits (711), Expect = 2e-79
 Identities = 158/386 (40%), Positives = 216/386 (55%), Gaps = 18/386 (4%)

Query: 1   MTDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDT-----TNFWAR 55
           MT +  +A  + LI   SVTPA+ G    +   L  LGF ++ +   +       N +AR
Sbjct: 1   MTATDPVANLQTLIRCPSVTPAEGGALTALDAMLTPLGFTVDRVTAREEGTAAIENLYAR 60

Query: 56  RGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVER 115
            G   P  +FAGHTDVVP G  + W  PPF   + +G L GRGA DMKG +AC + AV R
Sbjct: 61  LGRDGPHLMFAGHTDVVPVGDEAAWTHPPFAAEISNGELFGRGAVDMKGGIACFVAAVAR 120

Query: 116 FIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVV 175
            I +     GSI FL+T DEEGP INGT+++++    R E  D C+VGEP++   +GD++
Sbjct: 121 HIEKSGPPAGSISFLVTGDEEGPAINGTIKLLQWAAERGERWDACLVGEPTNPDRLGDMI 180

Query: 176 KNGRRGSITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQI 235
           K GRRGS++G + V G QGH AYPHLA+NPV   L     L    +D G   F P++ ++
Sbjct: 181 KIGRRGSLSGKITVHGVQGHAAYPHLADNPVRGLLQLTQALMDPPFDGGTDDFQPSNLEV 240

Query: 236 PNLQAGTGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHG-----------LDY 284
             +  G  A+NVIP +    FN RF+   T E ++  +   L+A               Y
Sbjct: 241 TTVDVGNPATNVIPAKASASFNIRFNDSWTVETLRAEILRRLEAAAGNGQLRPGRPPAKY 300

Query: 285 DVKWT-LSGQPFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELG 343
           D+ W       FLT    L+A++ +A+E V  ++PAL TTGGTSD RFI      VVE G
Sbjct: 301 DIVWADRPSHVFLTRNNALIASLSSAIESVAGRSPALSTTGGTSDARFIKDY-CPVVEFG 359

Query: 344 PVNATIHKVNECVRIADLEKLTDMYQ 369
            V  T+H V+E V +ADLE LT +YQ
Sbjct: 360 LVGQTMHMVDERVAVADLETLTAIYQ 385


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: 459
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 WP_042117802.1 RHE_RS02115 (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.4010.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.7e-125  402.5   0.0   1.1e-124  402.2   0.0    1.0  1  lcl|NCBI__GCF_000092045.1:WP_042117802.1  RHE_RS02115 succinyl-diaminopime


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092045.1:WP_042117802.1  RHE_RS02115 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.2   0.0  1.1e-124  1.1e-124       5     369 ..      10     390 ..       7     391 .. 0.96

  Alignments for each domain:
  == domain 1  score: 402.2 bits;  conditional E-value: 1.1e-124
                                 TIGR01246   5 akeLisrksvtPndagaqeliaerLkklgfeieilefed.....tknlwatrgteepvlvfaGhtDvvP 68 
                                               ++ Li+ +svtP++ ga+  +++ L+ lgf++++++  +     ++nl+a+ g + p+l+faGhtDvvP
  lcl|NCBI__GCF_000092045.1:WP_042117802.1  10 LQTLIRCPSVTPAEGGALTALDAMLTPLGFTVDRVTAREegtaaIENLYARLGRDGPHLMFAGHTDVVP 78 
                                               688*****************************9987643222226899999999*************** PP

                                 TIGR01246  69 aGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidG 137
                                               +G++ +W+ +pf++e+ +G l+grGa+Dmkg++a+fv+a+ r+++k     Gs+s+l+t Deeg ai+G
  lcl|NCBI__GCF_000092045.1:WP_042117802.1  79 VGDEAAWTHPPFAAEISNGELFGRGAVDMKGGIACFVAAVARHIEKSGPPAGSISFLVTGDEEGPAING 147
                                               ********************************************************************* PP

                                 TIGR01246 138 tkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavp 206
                                               t+k++++  er e  d ++vgeP+  ++lGD+ikiGrrGs++gk++++G+qGh aYPh+a+nPv  +++
  lcl|NCBI__GCF_000092045.1:WP_042117802.1 148 TIKLLQWAAERGERWDACLVGEPTNPDRLGDMIKIGRRGSLSGKITVHGVQGHAAYPHLADNPVRGLLQ 216
                                               ********************************************************************* PP

                                 TIGR01246 207 vlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh 275
                                               + ++l++  +D G++ f+ps+l+++ +++g+ a+nviP++++++fn+rf+ ++++e+l+ ++ + l++ 
  lcl|NCBI__GCF_000092045.1:WP_042117802.1 217 LTQALMDPPFDGGTDDFQPSNLEVTTVDVGNPATNVIPAKASASFNIRFNDSWTVETLRAEILRRLEAA 285
                                               ***************************************************************999998 PP

                                 TIGR01246 276 ...........kldYelewk.lsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklga 332
                                                            +Y++ w  + ++ flt+++ li+++ +aie v +++p+lst+GGtsDarfi+++ +
  lcl|NCBI__GCF_000092045.1:WP_042117802.1 286 agngqlrpgrpPAKYDIVWAdRPSHVFLTRNNALIASLSSAIESVAGRSPALSTTGGTSDARFIKDY-C 353
                                               8999999988889******736799******************************************.* PP

                                 TIGR01246 333 evvelGlvndtihkvneavkiedleklsevyekllee 369
                                                vve+Glv +t+h v+e+v ++dle l+++y++++ +
  lcl|NCBI__GCF_000092045.1:WP_042117802.1 354 PVVEFGLVGQTMHMVDERVAVADLETLTAIYQTFIDR 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.75
//
[ok]

This GapMind analysis is from Apr 10 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