Aligments for a candidate for dapD in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapD in Sinorhizobium meliloti 1021

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate SMc01732 SMc01732 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

Query= CharProtDB::CH_024869
         (274 letters)



>lcl|FitnessBrowser__Smeli:SMc01732 SMc01732
           2,3,4,5-tetrahydropyridine-2,6-carboxylate
           N-succinyltransferase
          Length = 296

 Score =  326 bits (835), Expect = 4e-94
 Identities = 175/280 (62%), Positives = 208/280 (74%), Gaps = 10/280 (3%)

Query: 1   MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKI-DGQWVTHQWL 59
           +  L   IETAFE R  +       V R+AV   + LLDSG +RVAE+  DG W  +QWL
Sbjct: 17  LASLSQTIETAFEGRDAVNTGTRGAV-RDAVETALNLLDSGKVRVAERSEDGTWTVNQWL 75

Query: 60  KKAVLLSFRINDNQVIEGA--ESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFI 117
           KKAVLLSFR+N  +++ G   E+ ++DKV  KF  +    F+K GFR VP   VR+ A+I
Sbjct: 76  KKAVLLSFRLNPMELVRGGPGEAVWWDKVASKFDGWSVNEFEKAGFRAVPNCVVRRSAYI 135

Query: 118 ARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTI 177
           A N VLMPS+VN+GAYV EGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTI
Sbjct: 136 APNAVLMPSFVNLGAYVGEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTI 195

Query: 178 IEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGN 237
           IEDNCFIGARSEVVEG IV EGSV+ MGV+IG+ST+I DR TGE+ YG VP  SVVV+G+
Sbjct: 196 IEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRATGEVMYGEVPPYSVVVAGS 255

Query: 238 LPS----KDGK--YSLYCAVIVKKVDAKTRGKVGINELLR 271
           + S     +G+   +LYCAVIVK+VD KTR K GINELLR
Sbjct: 256 MASGSTMANGQPAPNLYCAVIVKRVDEKTRSKTGINELLR 295


Lambda     K      H
   0.318    0.136    0.391 

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: 288
Number of extensions: 11
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: 274
Length of database: 296
Length adjustment: 26
Effective length of query: 248
Effective length of database: 270
Effective search space:    66960
Effective search space used:    66960
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate SMc01732 SMc01732 (2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase)
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

# 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/TIGR00965.hmm
# target sequence database:        /tmp/gapView.21724.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00965  [M=271]
Accession:   TIGR00965
Description: dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-126  407.4   0.7   1.7e-126  407.2   0.7    1.0  1  lcl|FitnessBrowser__Smeli:SMc01732  SMc01732 2,3,4,5-tetrahydropyrid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01732  SMc01732 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.2   0.7  1.7e-126  1.7e-126       2     269 ..      20     295 ..      19     296 .] 0.94

  Alignments for each domain:
  == domain 1  score: 407.2 bits;  conditional E-value: 1.7e-126
                           TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritdnqvlnd 75 
                                         l + ietafe r+ +  + +   v++av+ +++ ldsg++rvae+  dg w vn+w+kkavllsfr++  +++ +
  lcl|FitnessBrowser__Smeli:SMc01732  20 LSQTIETAFEGRDAVN-TGTRGAVRDAVETALNLLDSGKVRVAERSeDGTWTVNQWLKKAVLLSFRLNPMELVRG 93 
                                         6789*******98775.5667789*********************989*************************98 PP

                           TIGR00965  76 a..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatvgsca 148
                                         +  ++ ++dkva+kf  ++ +ef++ag+r+vp+ vvrr a+ia n vlmps+vn+gayv egtmvdtwatvgsca
  lcl|FitnessBrowser__Smeli:SMc01732  94 GpgEAVWWDKVASKFDGWSVNEFEKAGFRAVPNCVVRRSAYIAPNAVLMPSFVNLGAYVGEGTMVDTWATVGSCA 168
                                         533789********************************************************************* PP

                           TIGR00965 149 qigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdretgeiiyg 223
                                         qigknvhlsggvgiggvlep+qa p+iiedncfigarse+veg iv egsv+ mgvfig+stkivdr tge++yg
  lcl|FitnessBrowser__Smeli:SMc01732 169 QIGKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRATGEVMYG 243
                                         *************************************************************************** PP

                           TIGR00965 224 rvpagsvvvsgslps....kdgk..kslycavivkkvdaktrgkvsinellr 269
                                          vp +svvv+gs+ s     +g+  ++lycavivk+vd+ktr+k++inellr
  lcl|FitnessBrowser__Smeli:SMc01732 244 EVPPYSVVVAGSMASgstmANGQpaPNLYCAVIVKRVDEKTRSKTGINELLR 295
                                         *************98544335652257************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (296 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.20
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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