Alignments for a candidate for dapD in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Sinorhizobium fredii NGR234

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate YP_002824625.1 NGR_c00680 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= CharProtDB::CH_024869
         (274 letters)



>NCBI__GCF_000018545.1:YP_002824625.1
          Length = 285

 Score =  331 bits (849), Expect = 9e-96
 Identities = 175/280 (62%), Positives = 212/280 (75%), Gaps = 10/280 (3%)

Query: 1   MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEK-IDGQWVTHQWL 59
           +  L   IETAFE R  ++ +    + R+AV   + LLDSG +RVAE+  DG W  +QWL
Sbjct: 6   LASLSQTIETAFEDREAVSTSTRGAI-RDAVEAALNLLDSGKVRVAERGADGTWTVNQWL 64

Query: 60  KKAVLLSFRINDNQVIEGA--ESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFI 117
           KKAVLLSFR+N  ++++G   ES ++DKV  KF  +    F+K GFR VP   VR+ A+I
Sbjct: 65  KKAVLLSFRLNPMELVKGGPGESVWWDKVASKFDGWSVNEFEKAGFRAVPNCVVRRSAYI 124

Query: 118 ARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTI 177
           A N +LMPS+VN+GAYV EGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTI
Sbjct: 125 APNAILMPSFVNLGAYVGEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTI 184

Query: 178 IEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGN 237
           IEDNCFIGARSEVVEG IV EGSV+ MGV+IG+ST+I DR TGE+ YG VP  SVVV+G+
Sbjct: 185 IEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRATGEVTYGEVPPYSVVVAGS 244

Query: 238 LPS----KDGK--YSLYCAVIVKKVDAKTRGKVGINELLR 271
           +PS     +G+   +LYCAVIVK+VD KTR K GINELLR
Sbjct: 245 MPSGSTMANGQPAPNLYCAVIVKRVDEKTRSKTGINELLR 284


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: 286
Number of extensions: 9
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: 285
Length adjustment: 26
Effective length of query: 248
Effective length of database: 259
Effective search space:    64232
Effective search space used:    64232
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 YP_002824625.1 NGR_c00680 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate 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.10781.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-128  412.1   0.4   6.3e-128  411.9   0.4    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002824625.1  NGR_c00680 2,3,4,5-tetrahydropyr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002824625.1  NGR_c00680 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransfera
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.9   0.4  6.3e-128  6.3e-128       2     269 ..       9     284 ..       8     285 .] 0.94

  Alignments for each domain:
  == domain 1  score: 411.9 bits;  conditional E-value: 6.3e-128
                                 TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritd 69 
                                               l + ietafe r+ +  + +   +++av+ +++ ldsg++rvae+  dg w vn+w+kkavllsfr++ 
  lcl|NCBI__GCF_000018545.1:YP_002824625.1   9 LSQTIETAFEDREAVSTS-TRGAIRDAVEAALNLLDSGKVRVAERGaDGTWTVNQWLKKAVLLSFRLNP 76 
                                               6789********988755.56789*********************879********************* PP

                                 TIGR00965  70 nqvlnd..avnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegt 136
                                                +++++  +++ ++dkva+kf  ++ +ef++ag+r+vp+ vvrr a+ia n +lmps+vn+gayv egt
  lcl|NCBI__GCF_000018545.1:YP_002824625.1  77 MELVKGgpGESVWWDKVASKFDGWSVNEFEKAGFRAVPNCVVRRSAYIAPNAILMPSFVNLGAYVGEGT 145
                                               ****98335899********************************************************* PP

                                 TIGR00965 137 mvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvf 205
                                               mvdtwatvgscaqigknvhlsggvgiggvlep+qa p+iiedncfigarse+veg iv egsv+ mgvf
  lcl|NCBI__GCF_000018545.1:YP_002824625.1 146 MVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVF 214
                                               ********************************************************************* PP

                                 TIGR00965 206 igqstkivdretgeiiygrvpagsvvvsgslps....kdgk..kslycavivkkvdaktrgkvsinell 268
                                               ig+stkivdr tge+ yg vp +svvv+gs+ps     +g+  ++lycavivk+vd+ktr+k++inell
  lcl|NCBI__GCF_000018545.1:YP_002824625.1 215 IGKSTKIVDRATGEVTYGEVPPYSVVVAGSMPSgstmANGQpaPNLYCAVIVKRVDEKTRSKTGINELL 283
                                               ********************************9644335652257************************ PP

                                 TIGR00965 269 r 269
                                               r
  lcl|NCBI__GCF_000018545.1:YP_002824625.1 284 R 284
                                               9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (285 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: 00:00:00.00
# Mc/sec: 9.13
//
[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