Alignments for a candidate for dapD in Methylocystis bryophila S285

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Methylocystis bryophila S285

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_085770152.1 B1812_RS02260 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= CharProtDB::CH_024869
         (274 letters)



>NCBI__GCF_002117405.1:WP_085770152.1
          Length = 285

 Score =  338 bits (867), Expect = 8e-98
 Identities = 179/280 (63%), Positives = 210/280 (75%), Gaps = 13/280 (4%)

Query: 4   LQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQ-----WVTHQW 58
           L+++I  AFE RA ITP+    + R AV   + LLD G LRVAEKI+G+     W  HQW
Sbjct: 6   LESLITAAFEDRANITPSTQGDI-RHAVESALRLLDCGKLRVAEKIEGEEGPASWRVHQW 64

Query: 59  LKKAVLLSFRINDNQVIEGAE--SRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAF 116
           LKKAVLLSFR+ND  VI G    + ++DKVP KF  +        GFR VP A VR  A+
Sbjct: 65  LKKAVLLSFRLNDMNVIAGGPGGATWWDKVPSKFTGWGAKEHADGGFRSVPGAIVRHSAY 124

Query: 117 IARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPT 176
           +A   +LMPS+VN+GAYVD GTMVDTW TVGSCAQIGKNVHLSGGVGIGGVLEPLQANPT
Sbjct: 125 VAPGAILMPSFVNLGAYVDSGTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPT 184

Query: 177 IIEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSG 236
           IIED+CFIGARSEVVEGV++ +GSV+SMGV+IG ST++ DR TG++H G VP  SVVVSG
Sbjct: 185 IIEDDCFIGARSEVVEGVVIGKGSVLSMGVFIGASTKVIDRSTGKVHVGYVPPYSVVVSG 244

Query: 237 NLPSK---DGKY--SLYCAVIVKKVDAKTRGKVGINELLR 271
           N+P K   DG+   SLYCAVIVK VDA+TR K GINELLR
Sbjct: 245 NIPGKSLPDGQSGPSLYCAVIVKTVDAQTRAKTGINELLR 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: 280
Number of extensions: 10
Number of successful extensions: 5
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 WP_085770152.1 B1812_RS02260 (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.20855.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-124  398.6   0.1   8.1e-124  398.4   0.1    1.0  1  lcl|NCBI__GCF_002117405.1:WP_085770152.1  B1812_RS02260 2,3,4,5-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085770152.1  B1812_RS02260 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.4   0.1  8.1e-124  8.1e-124       3     269 ..       7     284 ..       5     285 .] 0.94

  Alignments for each domain:
  == domain 1  score: 398.4 bits;  conditional E-value: 8.1e-124
                                 TIGR00965   3 qkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgq.....wkvnewvkkavllsfr 66 
                                                  i  afe ra+i+p+++  ++++av+ +++ ld g+lrvaek++g+     w+v++w+kkavllsfr
  lcl|NCBI__GCF_002117405.1:WP_085770152.1   7 ESLITAAFEDRANITPSTQ-GDIRHAVESALRLLDCGKLRVAEKIEGEegpasWRVHQWLKKAVLLSFR 74 
                                               567999**********875.689**********************76445555**************** PP

                                 TIGR00965  67 itdnqvlnda..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvd 133
                                               ++d +v+ ++   + ++dkv++kf+ +  +e  + g+r vpga+vr+ a++a   +lmps+vn+gayvd
  lcl|NCBI__GCF_002117405.1:WP_085770152.1  75 LNDMNVIAGGpgGATWWDKVPSKFTGWGAKEHADGGFRSVPGAIVRHSAYVAPGAILMPSFVNLGAYVD 143
                                               *******98622689****************************************************** PP

                                 TIGR00965 134 egtmvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvism 202
                                                gtmvdtw tvgscaqigknvhlsggvgiggvleplqa+p+iied+cfigarse+vegv++ +gsv+sm
  lcl|NCBI__GCF_002117405.1:WP_085770152.1 144 SGTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDDCFIGARSEVVEGVVIGKGSVLSM 212
                                               ********************************************************************* PP

                                 TIGR00965 203 gvfigqstkivdretgeiiygrvpagsvvvsgslpsk...dgk..kslycavivkkvdaktrgkvsine 266
                                               gvfig stk++dr+tg+++ g vp +svvvsg++p k   dg+  +slycavivk vda+tr+k++ine
  lcl|NCBI__GCF_002117405.1:WP_085770152.1 213 GVFIGASTKVIDRSTGKVHVGYVPPYSVVVSGNIPGKslpDGQsgPSLYCAVIVKTVDAQTRAKTGINE 281
                                               *********************************99864445653379********************** PP

                                 TIGR00965 267 llr 269
                                               llr
  lcl|NCBI__GCF_002117405.1:WP_085770152.1 282 LLR 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.66
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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