Alignments for a candidate for DAPtransferase in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Desulfatiglans anilini DSM 4660

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_028320091.1 H567_RS0101850 LL-diaminopimelate aminotransferase

Query= BRENDA::A0LEA5
         (388 letters)



>NCBI__GCF_000422285.1:WP_028320091.1
          Length = 389

 Score =  558 bits (1437), Expect = e-163
 Identities = 260/385 (67%), Positives = 322/385 (83%)

Query: 3   FVKAERLKLLPPYLFQEIDRLKAELTAKGVDVINLGVGDPDLPTPDHIIARLKTAAEDPS 62
           F +AERLK LPPYLF+EIDR KAE+ A+GVD+I+LGVGDPDLPTP HII  LK A EDP 
Sbjct: 4   FERAERLKRLPPYLFKEIDRKKAEVKARGVDIIDLGVGDPDLPTPPHIIEVLKKAVEDPG 63

Query: 63  THQYPSYSGMNDFKVSVAGWYKRRFGVELDPLSEVLTLIGSKEGLAHFPLAVINPGDLAL 122
            H+YPSYSGM  FK +VA WY RRFGV+LDP +EV++LIGSKEG+AHFPLA I+PGD+AL
Sbjct: 64  NHRYPSYSGMGGFKEAVAEWYGRRFGVQLDPKTEVVSLIGSKEGIAHFPLAFIDPGDVAL 123

Query: 123 VPTPAYPVYHVATMFAGGESYFMPLVRENGFLPDLDSIPADVARRAKVMFINYPNNPTGA 182
           VPTPAYPVYH+ATMFAGGESYFMPL+++N FLPDLD+IP +VA RA++MFINYPNNPT A
Sbjct: 124 VPTPAYPVYHIATMFAGGESYFMPLLKKNDFLPDLDAIPGEVAGRARMMFINYPNNPTAA 183

Query: 183 TAERDFFEKVIAFAREYDVIVCHDAAYTEMAFGGYRPLSFLELPGAGEVGVEFHSLSKTY 242
            A+R FFE+V+AFA++ ++IVCHDAAYTEM + GY+P SFLE+PGA +VG+EFHSLSKTY
Sbjct: 184 VADRAFFERVVAFAKDKNLIVCHDAAYTEMGYDGYQPPSFLEVPGAKDVGLEFHSLSKTY 243

Query: 243 NMTGWRLGFAVGNADILAGLGQVKSNIDSGAFNAVQWAGITALEGDQGCVVEMQRIYKER 302
           NMTGWR+GFAVGN + + GLG +KSNIDSG F AVQ AGI A+ GDQ CV EM+ +Y  R
Sbjct: 244 NMTGWRIGFAVGNREAVDGLGAIKSNIDSGVFQAVQMAGIEAIAGDQACVDEMRTVYTRR 303

Query: 303 LDILIEGLKRIGLHPEVPRATFYVWCPTPPGYSSKDFSSLLLREAGIVATPGSGFGAPGE 362
            D++++GL++ G    VPRATFY+W   P GY+S   ++ LL EAG+V TPG+GFG PGE
Sbjct: 304 RDLMVKGLEKAGFRLRVPRATFYLWVEVPAGYTSAQVATRLLEEAGLVVTPGNGFGEPGE 363

Query: 363 GYIRMALTVDKERVREAVERMRKLS 387
           GY R+ALT ++ER+ EA+ER++KL+
Sbjct: 364 GYFRIALTQNRERLAEAIERLQKLN 388


Lambda     K      H
   0.321    0.140    0.423 

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: 624
Number of extensions: 28
Number of successful extensions: 1
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: 388
Length of database: 389
Length adjustment: 30
Effective length of query: 358
Effective length of database: 359
Effective search space:   128522
Effective search space used:   128522
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_028320091.1 H567_RS0101850 (LL-diaminopimelate aminotransferase)
to HMM TIGR03540 (LL-diaminopimelate aminotransferase (EC 2.6.1.83))

# 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/TIGR03540.hmm
# target sequence database:        /tmp/gapView.2927.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03540  [M=383]
Accession:   TIGR03540
Description: DapC_direct: LL-diaminopimelate aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-195  635.3   0.0   1.9e-195  635.1   0.0    1.0  1  lcl|NCBI__GCF_000422285.1:WP_028320091.1  H567_RS0101850 LL-diaminopimelat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000422285.1:WP_028320091.1  H567_RS0101850 LL-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  635.1   0.0  1.9e-195  1.9e-195       2     382 ..       6     386 ..       5     387 .. 1.00

  Alignments for each domain:
  == domain 1  score: 635.1 bits;  conditional E-value: 1.9e-195
                                 TIGR03540   2 laerleklPPylfaeidklkaekkakGvdvidlgiGdPdlptpkeivealkkaaekpenhryPsyeGll 70 
                                                aerl++lPPylf eid++kae+ka+Gvd+idlg+GdPdlptp +i+e lkka+e+p nhryPsy+G+ 
  lcl|NCBI__GCF_000422285.1:WP_028320091.1   6 RAERLKRLPPYLFKEIDRKKAEVKARGVDIIDLGVGDPDLPTPPHIIEVLKKAVEDPGNHRYPSYSGMG 74 
                                               69******************************************************************* PP

                                 TIGR03540  71 ayrkavadwykkrfgveldpetevlsliGskeGiahlplafvnpGdivlvpdPgyPvykistllaggep 139
                                                +++ava+wy +rfgv+ldp+tev+sliGskeGiah+plaf++pGd++lvp P+yPvy+i+t++agge+
  lcl|NCBI__GCF_000422285.1:WP_028320091.1  75 GFKEAVAEWYGRRFGVQLDPKTEVVSLIGSKEGIAHFPLAFIDPGDVALVPTPAYPVYHIATMFAGGES 143
                                               ********************************************************************* PP

                                 TIGR03540 140 yelPlkeendflPdldaipedvlkkakilflnyPnnPtsavadkeffkevvefakeyniivvhdaayse 208
                                               y +Pl+++ndflPdldaip +v+ +a+++f+nyPnnPt+avad+ ff++vv+fak++n+iv+hdaay+e
  lcl|NCBI__GCF_000422285.1:WP_028320091.1 144 YFMPLLKKNDFLPDLDAIPGEVAGRARMMFINYPNNPTAAVADRAFFERVVAFAKDKNLIVCHDAAYTE 212
                                               ********************************************************************* PP

                                 TIGR03540 209 ivfdeykalsflevdgakdvaielhslsktynmtGWrigfavGnkeliaalgkvksnvdsGvfqaiqea 277
                                               + +d+y+++sflev+gakdv++e+hslsktynmtGWrigfavGn+e +++lg +ksn+dsGvfqa+q a
  lcl|NCBI__GCF_000422285.1:WP_028320091.1 213 MGYDGYQPPSFLEVPGAKDVGLEFHSLSKTYNMTGWRIGFAVGNREAVDGLGAIKSNIDSGVFQAVQMA 281
                                               ********************************************************************* PP

                                 TIGR03540 278 aiaaleeeeevvkelrkvykkrrdllvealkkiGldvkkpkatfylWvkvPeGytsaefakklleeagv 346
                                               +i+a+ +++++v+e+r vy +rrdl+v++l+k G+ ++ p+atfylWv+vP+Gytsa+ a++lleeag+
  lcl|NCBI__GCF_000422285.1:WP_028320091.1 282 GIEAIAGDQACVDEMRTVYTRRRDLMVKGLEKAGFRLRVPRATFYLWVEVPAGYTSAQVATRLLEEAGL 350
                                               ********************************************************************* PP

                                 TIGR03540 347 vvtpGvgfGesGeGyirisltvseerlkeaverlkk 382
                                               vvtpG+gfGe GeGy+ri+lt+++erl+ea+erl+k
  lcl|NCBI__GCF_000422285.1:WP_028320091.1 351 VVTPGNGFGEPGEGYFRIALTQNRERLAEAIERLQK 386
                                               **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (383 nodes)
Target sequences:                          1  (389 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: 9.93
//
[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