Alignments for a candidate for dapD in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Magnetospirillum magneticum AMB-1

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Tetrahydrodipicolinate N-succinyltransferase; THDP succinyltransferase; THP succinyltransferase; Tetrahydropicolinate succinylase; EC 2.3.1.117 (characterized)
to candidate WP_011386227.1 AMB_RS19595 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>NCBI__GCF_000009985.1:WP_011386227.1
          Length = 280

 Score =  341 bits (875), Expect = 9e-99
 Identities = 182/275 (66%), Positives = 214/275 (77%), Gaps = 8/275 (2%)

Query: 4   LQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEK-IDGQWVTHQWLKKA 62
           L+  I++A+E R  I       V R+AV   +  LDSG+LRVA K  DG+WV +QWLKKA
Sbjct: 6   LEKTIDAAWEARDGINLQTKGEV-RDAVEAALDALDSGSLRVAAKGDDGKWVVNQWLKKA 64

Query: 63  VLLSFRINDNKVM-DGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNT 121
           VLLSFR++DNKVM DG  T ++DKVP KF  +D++RF+  GFR VP A VR+ A+IA   
Sbjct: 65  VLLSFRLSDNKVMGDGPGTTWFDKVPTKFEGWDDSRFRAAGFRAVPGAVVRRSAYIAPGV 124

Query: 122 VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDN 181
           VLMPS+VN+GA+V  GTMVDTWATVGSCAQIGKNVH+SGG GIGGVLEPLQA P IIEDN
Sbjct: 125 VLMPSFVNLGAHVGSGTMVDTWATVGSCAQIGKNVHISGGAGIGGVLEPLQAGPVIIEDN 184

Query: 182 CFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSK 241
           CFIGAR+EV EGVIVE G+V+SMGVY+G ST+I DRETGEI  GRVPA SVVVSG +P K
Sbjct: 185 CFIGARAEVAEGVIVETGAVLSMGVYIGASTKIVDRETGEIFMGRVPAYSVVVSGTMPGK 244

Query: 242 ---DGS--YSLYCAVIVKKVDAKTRGKVGINELLR 271
              DG+    LYCAVIVK+VD +TR KVGINELLR
Sbjct: 245 PFPDGTPGPGLYCAVIVKRVDERTRSKVGINELLR 279


Lambda     K      H
   0.318    0.136    0.393 

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: 281
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: 280
Length adjustment: 25
Effective length of query: 249
Effective length of database: 255
Effective search space:    63495
Effective search space used:    63495
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 WP_011386227.1 AMB_RS19595 (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.6303.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-131  422.3   0.2   4.8e-131  422.1   0.2    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386227.1  AMB_RS19595 2,3,4,5-tetrahydropy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386227.1  AMB_RS19595 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.1   0.2  4.8e-131  4.8e-131       2     269 ..       6     279 ..       5     280 .] 0.95

  Alignments for each domain:
  == domain 1  score: 422.1 bits;  conditional E-value: 4.8e-131
                                 TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritd 69 
                                               l k i+ a+e r+ i   + + +v++av+ ++  ldsg lrva k  dg+w+vn+w+kkavllsfr++d
  lcl|NCBI__GCF_000009985.1:WP_011386227.1   6 LEKTIDAAWEARDGINLQT-KGEVRDAVEAALDALDSGSLRVAAKGdDGKWVVNQWLKKAVLLSFRLSD 73 
                                               6799*********998765.5799*********************8799******************** PP

                                 TIGR00965  70 nqvlnda.vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtm 137
                                               n+v+ d+  + +fdkv+tkf  +d+++f+ ag+r+vpgavvrr a+ia  vvlmps+vn+ga+v  gtm
  lcl|NCBI__GCF_000009985.1:WP_011386227.1  74 NKVMGDGpGTTWFDKVPTKFEGWDDSRFRAAGFRAVPGAVVRRSAYIAPGVVLMPSFVNLGAHVGSGTM 142
                                               ****8872578********************************************************** PP

                                 TIGR00965 138 vdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfi 206
                                               vdtwatvgscaqigknvh+sgg+giggvleplqa pviiedncfigar+e++egvive g+v+smgv+i
  lcl|NCBI__GCF_000009985.1:WP_011386227.1 143 VDTWATVGSCAQIGKNVHISGGAGIGGVLEPLQAGPVIIEDNCFIGARAEVAEGVIVETGAVLSMGVYI 211
                                               ********************************************************************* PP

                                 TIGR00965 207 gqstkivdretgeiiygrvpagsvvvsgslpsk...dgk..kslycavivkkvdaktrgkvsinellr 269
                                               g stkivdretgei+ grvpa+svvvsg++p k   dg   ++lycavivk+vd++tr+kv+inellr
  lcl|NCBI__GCF_000009985.1:WP_011386227.1 212 GASTKIVDRETGEIFMGRVPAYSVVVSGTMPGKpfpDGTpgPGLYCAVIVKRVDERTRSKVGINELLR 279
                                               *******************************864557872258************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (280 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 7.18
//
[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