Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Miyazaki F

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)

Query= BRENDA::O66630
         (387 letters)



>FitnessBrowser__Miya:8499593
          Length = 389

 Score =  472 bits (1215), Expect = e-138
 Identities = 236/386 (61%), Positives = 289/386 (74%), Gaps = 2/386 (0%)

Query: 2   FEFSDRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPE 61
           F+ +DRL  LPPYLFA +D+ K E   +GVD+I LG+GDPDMPTP  I+EA KKA+E P 
Sbjct: 4   FKLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVERPA 63

Query: 62  NHKYPSYVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDIVL 121
           NH+YPSYVG  EFR+ VA+WY RRF V LDP TEVI LIGSKEGIAHFPLAFVNPGD+VL
Sbjct: 64  NHQYPSYVGMLEFRQEVANWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGDLVL 123

Query: 122 CPDPAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTSA 181
              P YPVY I   F GG    +PL EEN++LPDLD+IP     +AK+I++NYPNNPT+A
Sbjct: 124 VCTPNYPVYHIATGFVGGEVQFIPLVEENDYLPDLDAIPAATWDRAKMIFVNYPNNPTAA 183

Query: 182 PPTLEFYKKLVDWAKEYNVIIASDNAYSEIYTGQ-EKPPSILQVPGAKDVAIEFHSLSKT 240
                FY+KL+   +++NVIIA D AY+E+Y  + +KP SIL+V GAKDV IEFHSLSKT
Sbjct: 184 TAPRAFYEKLIGICRKHNVIIAHDTAYTEVYYDENDKPMSILEVEGAKDVTIEFHSLSKT 243

Query: 241 YNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRE 300
           YNMTGWR+GMAVGN  LVAGLGKVK NVDSG F AVQ+A IVAL   ++   ++R +YR+
Sbjct: 244 YNMTGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRELRGIYRK 303

Query: 301 RKKIMTEALEKIGLEIYRSDYTFYLWIKVPEGY-TSAEFVGRLIDEAGIVCTPGNGFGEY 359
           R+ ++  AL K+G+        FY+W KVP GY +SAEFV  ++++ G+V TPGNGFG  
Sbjct: 304 RRDVVVAALNKVGIACRVPTAAFYIWAKVPAGYGSSAEFVTAVLEKTGVVLTPGNGFGTP 363

Query: 360 GEGYFRISLTVPTERLLEAAERIKNL 385
           GEGYFRISLTV T+RL EA  RI NL
Sbjct: 364 GEGYFRISLTVDTDRLEEAVSRIANL 389


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: 506
Number of extensions: 17
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: 389
Length adjustment: 30
Effective length of query: 357
Effective length of database: 359
Effective search space:   128163
Effective search space used:   128163
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 8499593 DvMF_0361 (LL-diaminopimelate aminotransferase (RefSeq))
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.30703.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.2e-192  623.3   0.0   8.1e-192  623.2   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499593  DvMF_0361 LL-diaminopimelate ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499593  DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.2   0.0  8.1e-192  8.1e-192       1     382 [.       5     388 ..       5     389 .] 0.99

  Alignments for each domain:
  == domain 1  score: 623.2 bits;  conditional E-value: 8.1e-192
                         TIGR03540   1 klaerleklPPylfaeidklkaekkakGvdvidlgiGdPdlptpkeivealkkaaekpenhryPsyeGllayrkava 77 
                                       kla+rl++lPPylfa idk+kae++a+Gvd+i+lgiGdPd+ptp+ i+ea+kka+e+p+nh+yPsy+G+l++r++va
  lcl|FitnessBrowser__Miya:8499593   5 KLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVERPANHQYPSYVGMLEFRQEVA 81 
                                       589************************************************************************** PP

                         TIGR03540  78 dwykkrfgveldpetevlsliGskeGiahlplafvnpGdivlvpdPgyPvykistllaggepyelPlkeendflPdl 154
                                       +wy +rfgv ldp+tev++liGskeGiah+plafvnpGd+vlv+ P yPvy+i+t ++gge++ +Pl eend+lPdl
  lcl|FitnessBrowser__Miya:8499593  82 NWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGDLVLVCTPNYPVYHIATGFVGGEVQFIPLVEENDYLPDL 158
                                       ***************************************************************************** PP

                         TIGR03540 155 daipedvlkkakilflnyPnnPtsavadkeffkevvefakeyniivvhdaayseivfdey.kalsflevdgakdvai 230
                                       daip+ ++ +ak++f+nyPnnPt+a+a++ f+++++ +++++n+i++hd+ay+e+++de+ k++s+lev+gakdv+i
  lcl|FitnessBrowser__Miya:8499593 159 DAIPAATWDRAKMIFVNYPNNPTAATAPRAFYEKLIGICRKHNVIIAHDTAYTEVYYDENdKPMSILEVEGAKDVTI 235
                                       *********************************************************9753799************* PP

                         TIGR03540 231 elhslsktynmtGWrigfavGnkeliaalgkvksnvdsGvfqaiqeaaiaaleeeeevvkelrkvykkrrdllveal 307
                                       e+hslsktynmtGWr+g+avGn++l+a+lgkvk+nvdsG+fqa+qea+i+al++ +++ +elr +y+krrd++v+al
  lcl|FitnessBrowser__Miya:8499593 236 EFHSLSKTYNMTGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRELRGIYRKRRDVVVAAL 312
                                       ***************************************************************************** PP

                         TIGR03540 308 kkiGldvkkpkatfylWvkvPeGy.tsaefakklleeagvvvtpGvgfGesGeGyirisltvseerlkeaverlkk 382
                                       +k+G+ ++ p a+fy+W+kvP+Gy +saef++ +le++gvv+tpG+gfG+ GeGy+risltv+++rl+eav+r+++
  lcl|FitnessBrowser__Miya:8499593 313 NKVGIACRVPTAAFYIWAKVPAGYgSSAEFVTAVLEKTGVVLTPGNGFGTPGEGYFRISLTVDTDRLEEAVSRIAN 388
                                       ***********************94578**********************************************87 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.12
//
[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