Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Hildenborough

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 207114 DVU1655 aminotransferase, classes I and II

Query= BRENDA::O66630
         (387 letters)



>MicrobesOnline__882:207114
          Length = 388

 Score =  479 bits (1232), Expect = e-140
 Identities = 237/385 (61%), Positives = 290/385 (75%), Gaps = 1/385 (0%)

Query: 2   FEFSDRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPE 61
           F+ +DRL  LPPYLFA +D+ K E   +GVD+I LG+GDPDM TP  I+EA K+A+  P 
Sbjct: 4   FKLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMATPGFIIEAMKEAIARPA 63

Query: 62  NHKYPSYVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDIVL 121
           NH+YPSYVG   FR+ VA+WY RRF V LDP TEVI LIGSKEGIAHFP AF+NPGD+VL
Sbjct: 64  NHQYPSYVGMLAFRQEVANWYDRRFGVSLDPATEVIGLIGSKEGIAHFPFAFINPGDLVL 123

Query: 122 CPDPAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTSA 181
              P YPVY I   FAGG    VPL EEN+FLPDLD+IPED  K+AK+I++NYPNNPT+A
Sbjct: 124 VCTPNYPVYHIATGFAGGEVQFVPLLEENDFLPDLDAIPEDTWKRAKMIFVNYPNNPTAA 183

Query: 182 PPTLEFYKKLVDWAKEYNVIIASDNAYSEIYTGQE-KPPSILQVPGAKDVAIEFHSLSKT 240
              L FY+KLVD  + ++VIIA D AY+EIY  ++ +PPSIL VPGAKDVAIEFHSLSKT
Sbjct: 184 TAPLGFYEKLVDICRRFDVIIAHDTAYTEIYYDEDNRPPSILSVPGAKDVAIEFHSLSKT 243

Query: 241 YNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRE 300
           YNMTGWR+GMAVGN  LVAGLGK+K N+DSG F AVQ+A IVAL   ++   ++R +YR+
Sbjct: 244 YNMTGWRVGMAVGNPTLVAGLGKIKENMDSGIFQAVQEASIVALRDGDDFCRELRGIYRQ 303

Query: 301 RKKIMTEALEKIGLEIYRSDYTFYLWIKVPEGYTSAEFVGRLIDEAGIVCTPGNGFGEYG 360
           R+  +  AL K G++      TFY+W +VP+G+TSA+FV R++ E G+V TPGNGFG  G
Sbjct: 304 RRDTVINALHKAGIQCRVPQATFYVWARVPQGHTSADFVTRVLQETGVVVTPGNGFGTPG 363

Query: 361 EGYFRISLTVPTERLLEAAERIKNL 385
           EG+FRISLTV   RL EA  RI  L
Sbjct: 364 EGFFRISLTVDNARLEEAVSRIAKL 388


Lambda     K      H
   0.317    0.139    0.413 

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: 508
Number of extensions: 20
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: 387
Length of database: 388
Length adjustment: 30
Effective length of query: 357
Effective length of database: 358
Effective search space:   127806
Effective search space used:   127806
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 207114 DVU1655 (aminotransferase, classes I and II)
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.2372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.8e-191  621.4   0.0   3.2e-191  621.2   0.0    1.0  1  lcl|MicrobesOnline__882:207114  DVU1655 aminotransferase, classe


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207114  DVU1655 aminotransferase, classes I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.2   0.0  3.2e-191  3.2e-191       1     382 [.       5     387 ..       5     388 .] 0.99

  Alignments for each domain:
  == domain 1  score: 621.2 bits;  conditional E-value: 3.2e-191
                       TIGR03540   1 klaerleklPPylfaeidklkaekkakGvdvidlgiGdPdlptpkeivealkkaaekpenhryPsyeGllayrkavadw 79 
                                     kla+rl++lPPylfa idk+kae++a+Gvd+i+lgiGdPd++tp  i+ea+k+a+ +p+nh+yPsy+G+la+r++va+w
  lcl|MicrobesOnline__882:207114   5 KLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMATPGFIIEAMKEAIARPANHQYPSYVGMLAFRQEVANW 83 
                                     589**************************************************************************** PP

                       TIGR03540  80 ykkrfgveldpetevlsliGskeGiahlplafvnpGdivlvpdPgyPvykistllaggepyelPlkeendflPdldaip 158
                                     y +rfgv ldp tev++liGskeGiah+p+af+npGd+vlv+ P yPvy+i+t +agge++ +Pl+eendflPdldaip
  lcl|MicrobesOnline__882:207114  84 YDRRFGVSLDPATEVIGLIGSKEGIAHFPFAFINPGDLVLVCTPNYPVYHIATGFAGGEVQFVPLLEENDFLPDLDAIP 162
                                     ******************************************************************************* PP

                       TIGR03540 159 edvlkkakilflnyPnnPtsavadkeffkevvefakeyniivvhdaayseivfde.ykalsflevdgakdvaielhsls 236
                                     ed++k+ak++f+nyPnnPt+a+a+  f++++v++++  ++i++hd+ay+ei++de ++++s+l+v+gakdvaie+hsls
  lcl|MicrobesOnline__882:207114 163 EDTWKRAKMIFVNYPNNPTAATAPLGFYEKLVDICRRFDVIIAHDTAYTEIYYDEdNRPPSILSVPGAKDVAIEFHSLS 241
                                     *****************************************************8636899******************* PP

                       TIGR03540 237 ktynmtGWrigfavGnkeliaalgkvksnvdsGvfqaiqeaaiaaleeeeevvkelrkvykkrrdllvealkkiGldvk 315
                                     ktynmtGWr+g+avGn +l+a+lgk+k+n+dsG+fqa+qea+i+al++ +++ +elr +y++rrd++++al+k G++++
  lcl|MicrobesOnline__882:207114 242 KTYNMTGWRVGMAVGNPTLVAGLGKIKENMDSGIFQAVQEASIVALRDGDDFCRELRGIYRQRRDTVINALHKAGIQCR 320
                                     ******************************************************************************* PP

                       TIGR03540 316 kpkatfylWvkvPeGytsaefakklleeagvvvtpGvgfGesGeGyirisltvseerlkeaverlkk 382
                                      p+atfy+W++vP+G tsa+f++++l+e+gvvvtpG+gfG+ GeG++risltv++ rl+eav+r++k
  lcl|MicrobesOnline__882:207114 321 VPQATFYVWARVPQGHTSADFVTRVLQETGVVVTPGNGFGTPGEGFFRISLTVDNARLEEAVSRIAK 387
                                     *****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (383 nodes)
Target sequences:                          1  (388 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: 10.53
//
[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