Aligments for a candidate for dapD in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapD in Caulobacter crescentus NA1000

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 CCNA_00283 CCNA_00283 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00283 CCNA_00283
           2,3,4,5-tetrahydropyridine-2-carboxylate
           N-succinyltransferase
          Length = 286

 Score =  360 bits (924), Expect = e-104
 Identities = 185/276 (67%), Positives = 214/276 (77%), Gaps = 6/276 (2%)

Query: 1   MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLK 60
           +  LQ  IE+A+E RADI+ A    V R AV++ + LLDSG  RVAEKIDG+W THQWLK
Sbjct: 11  LADLQTEIEAAWEARADISAATTGPV-RTAVDEALRLLDSGEARVAEKIDGEWFTHQWLK 69

Query: 61  KAVLLSFRINDNKVM-----DGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGA 115
           KAVLLSFR+N N VM      G    ++DKVP KF  +D  +F+  GFR VP A VR+GA
Sbjct: 70  KAVLLSFRLNPNTVMRSGALGGGVGPWWDKVPNKFDGWDAPQFEAGGFRAVPGAIVRRGA 129

Query: 116 FIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANP 175
            I +N +LMPS+VNIG YVDEGTMVDTW TVGSCAQIGKNVHLSGGVGIGGVLEPLQANP
Sbjct: 130 HIGKNVILMPSFVNIGGYVDEGTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANP 189

Query: 176 TIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVS 235
           TIIEDNCFIGARSEVVEGV+V EGSV+SMGV++  ST+I DR+TG +H G+VP  SVVV 
Sbjct: 190 TIIEDNCFIGARSEVVEGVVVGEGSVLSMGVFISASTKIVDRKTGAVHIGKVPPYSVVVP 249

Query: 236 GNLPSKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
           GNLP  +G   LYCAVIVK VDA+TR K  IN+LLR
Sbjct: 250 GNLPDPNGGPGLYCAVIVKTVDAQTRSKTSINDLLR 285


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: 276
Number of extensions: 4
Number of successful extensions: 2
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: 286
Length adjustment: 26
Effective length of query: 248
Effective length of database: 260
Effective search space:    64480
Effective search space used:    64480
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 CCNA_00283 CCNA_00283 (2,3,4,5-tetrahydropyridine-2-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.14539.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-134  431.6   0.1   7.3e-134  431.4   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00283  CCNA_00283 2,3,4,5-tetrahydropyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00283  CCNA_00283 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.4   0.1  7.3e-134  7.3e-134       2     269 ..      14     285 ..      13     286 .] 0.96

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 7.3e-134
                             TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdnqvln 74 
                                           lq +ie a+e ra+i  a++   v+ av e+++ ldsg  rvaek+dg+w +++w+kkavllsfr++ n v+ 
  lcl|FitnessBrowser__Caulo:CCNA_00283  14 LQTEIEAAWEARADISAATT-GPVRTAVDEALRLLDSGEARVAEKIDGEWFTHQWLKKAVLLSFRLNPNTVMR 85 
                                           799************98765.568*********************************************9987 PP

                             TIGR00965  75 .....davnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwa 142
                                                ++v  ++dkv+ kf  +d  +f+  g+r+vpga+vrrga+i knv+lmps+vnig yvdegtmvdtw 
  lcl|FitnessBrowser__Caulo:CCNA_00283  86 sgalgGGVGPWWDKVPNKFDGWDAPQFEAGGFRAVPGAIVRRGAHIGKNVILMPSFVNIGGYVDEGTMVDTWV 158
                                           2222256889*************************************************************** PP

                             TIGR00965 143 tvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdr 215
                                           tvgscaqigknvhlsggvgiggvleplqa+p+iiedncfigarse+vegv+v egsv+smgvfi  stkivdr
  lcl|FitnessBrowser__Caulo:CCNA_00283 159 TVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVVVGEGSVLSMGVFISASTKIVDR 231
                                           ************************************************************************* PP

                             TIGR00965 216 etgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269
                                           +tg ++ g+vp +svvv+g+lp  +g ++lycavivk vda+tr+k+sin+llr
  lcl|FitnessBrowser__Caulo:CCNA_00283 232 KTGAVHIGKVPPYSVVVPGNLPDPNGGPGLYCAVIVKTVDAQTRSKTSINDLLR 285
                                           *****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (286 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: 00:00:00.01
# Mc/sec: 6.25
//
[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