Alignments for a candidate for dapD in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Azospirillum brasilense Sp245

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 AZOBR_RS03475 AZOBR_RS03475 2 3 4 5-tetrahydropyridine-2 6-carboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__azobra:AZOBR_RS03475
          Length = 280

 Score =  334 bits (857), Expect = 1e-96
 Identities = 173/275 (62%), Positives = 208/275 (75%), Gaps = 8/275 (2%)

Query: 4   LQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAV 63
           L++ + +A+E R D    +     R+AV + +  LDSG LRVA+K D  WV +QWLKKAV
Sbjct: 6   LESAVNAAWETR-DTLNVSTKGAVRDAVEEALSGLDSGDLRVAQKTDAGWVVNQWLKKAV 64

Query: 64  LLSFRINDNKVMDGAE--TRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNT 121
           LLSFR+N N+ + GA     +YDKVP KF  + EA+FQ  GFR VP A VR+ A++A N 
Sbjct: 65  LLSFRLNANETIPGAPGGASWYDKVPPKFEGWSEAQFQAAGFRAVPGAVVRRSAYVAPNV 124

Query: 122 VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDN 181
           +LMPS+VN+GAYVD GTMVDTW TVGSCAQIGKNVHLSGGVGIGGVLEPLQANP IIED+
Sbjct: 125 ILMPSFVNVGAYVDSGTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDD 184

Query: 182 CFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSK 241
           CF+GARSEVVEGVIVE G+V+SMGV++  ST+I DR TGE+  GRVPA SVVV G LP K
Sbjct: 185 CFVGARSEVVEGVIVERGAVLSMGVFISASTKIIDRNTGEVFVGRVPAYSVVVPGTLPGK 244

Query: 242 ---DGS--YSLYCAVIVKKVDAKTRGKVGINELLR 271
              DG+    LYCAVIVK+VD +TR K  IN+LLR
Sbjct: 245 PLPDGTPGPGLYCAVIVKRVDEQTRAKTSINDLLR 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: 274
Number of extensions: 10
Number of successful extensions: 3
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 AZOBR_RS03475 AZOBR_RS03475 (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.619.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-131  424.1   0.1   1.4e-131  423.9   0.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03475  AZOBR_RS03475 2 3 4 5-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03475  AZOBR_RS03475 2 3 4 5-tetrahydropyridine-2 6-carboxylate N-succinyltransfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.9   0.1  1.4e-131  1.4e-131       2     269 ..       6     279 ..       5     280 .] 0.94

  Alignments for each domain:
  == domain 1  score: 423.9 bits;  conditional E-value: 1.4e-131
                                 TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdn 70 
                                               l   ++ a+e+r+ +  ++ +  v++av+e+++ ldsg lrva+k d+ w+vn+w+kkavllsfr++ n
  lcl|FitnessBrowser__azobra:AZOBR_RS03475   6 LESAVNAAWETRDTLNVST-KGAVRDAVEEALSGLDSGDLRVAQKTDAGWVVNQWLKKAVLLSFRLNAN 73 
                                               5667899****98776655.6789********************************************* PP

                                 TIGR00965  71 qvlnda..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtm 137
                                               + + +a   ++++dkv++kf  ++e++f+ ag+r+vpgavvrr a++a nv+lmps+vn+gayvd gtm
  lcl|FitnessBrowser__azobra:AZOBR_RS03475  74 ETIPGApgGASWYDKVPPKFEGWSEAQFQAAGFRAVPGAVVRRSAYVAPNVILMPSFVNVGAYVDSGTM 142
                                               ***88622689********************************************************** PP

                                 TIGR00965 138 vdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfi 206
                                               vdtw tvgscaqigknvhlsggvgiggvleplqa+pviied+cf+garse+vegvive g+v+smgvfi
  lcl|FitnessBrowser__azobra:AZOBR_RS03475 143 VDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDDCFVGARSEVVEGVIVERGAVLSMGVFI 211
                                               ********************************************************************* PP

                                 TIGR00965 207 gqstkivdretgeiiygrvpagsvvvsgslpsk...dgk..kslycavivkkvdaktrgkvsinellr 269
                                                 stki+dr+tge++ grvpa+svvv+g+lp k   dg   ++lycavivk+vd++tr+k+sin+llr
  lcl|FitnessBrowser__azobra:AZOBR_RS03475 212 SASTKIIDRNTGEVFVGRVPAYSVVVPGTLPGKplpDGTpgPGLYCAVIVKRVDEQTRAKTSINDLLR 279
                                               ******************************9864457872258************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.81
//
[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