Alignments for a candidate for DAPtransferase in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Bacteroides thetaiotaomicron VPI-5482

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 350075 BT0547 aspartate aminotransferase (NCBI ptt file)

Query= BRENDA::Q5LC03
         (410 letters)



>FitnessBrowser__Btheta:350075
          Length = 410

 Score =  777 bits (2007), Expect = 0.0
 Identities = 369/410 (90%), Positives = 395/410 (96%)

Query: 1   MALVNEHFLKLPGSYLFSDIAKKVNTFKITHPKRDIIRLGIGDVTRPLPKACIEAMHKAV 60
           MALVNEHFLKLPGSYLFSDIAKKVNTFKITHPK+DIIRLGIGDVT+PLPKACIEAMHKAV
Sbjct: 1   MALVNEHFLKLPGSYLFSDIAKKVNTFKITHPKQDIIRLGIGDVTQPLPKACIEAMHKAV 60

Query: 61  EEMTSAETFRGYGPEQGYDFLIEAIIKNDYAPRGIHLSPTEVFVNDGAKSDTGNIGDILR 120
           EE+ S +TFRGYGPEQGYDFLIEAIIKND+APRGIH SP+E+FVNDGAKSDTGNIGDILR
Sbjct: 61  EELASKDTFRGYGPEQGYDFLIEAIIKNDFAPRGIHFSPSEIFVNDGAKSDTGNIGDILR 120

Query: 121 HDNSVGVTDPIYPVYIDSNVMCGRAGVLDTESGKWSNVTYMPCTAENHFIPAIPEKRIDI 180
           HDNSVGVTDPIYPVYIDSNVMCGRAGVL+  +GKWSNVTYMPCT+EN FIP IP+KRIDI
Sbjct: 121 HDNSVGVTDPIYPVYIDSNVMCGRAGVLEEGTGKWSNVTYMPCTSENDFIPEIPDKRIDI 180

Query: 181 VYLCYPNNPTGTTLTKAELKKWVDYALANDTLILFDAAYEAYIREPDIPHSIYEIKGAKK 240
           VYLCYPNNPTGTTLTK ELKKWVDYALANDTLILFDAAYEAYI++ D+PHSIYEIKGAKK
Sbjct: 181 VYLCYPNNPTGTTLTKPELKKWVDYALANDTLILFDAAYEAYIQDADVPHSIYEIKGAKK 240

Query: 241 CAIEFRSFSKTAGFTGVRCGYTVVPKELTAATLEGERIPLNRLWNRRQCTKFNGTSYITQ 300
           CAIEFRSFSKTAGFTGVRCGYTVVPKELTAATLEG+RIPLN+LWNRRQCTKFNGTSYITQ
Sbjct: 241 CAIEFRSFSKTAGFTGVRCGYTVVPKELTAATLEGDRIPLNKLWNRRQCTKFNGTSYITQ 300

Query: 301 RAAEAIYTPEGKEQIQETINYYMTNARIMKEGLESTGLKVYGGVNAPYLWVKTPKGTSSW 360
           RAAEA+Y+ EGK QI+ETINYYM+NA+IMKEGLE+TGLKVYGGVNAPYLWVKTP G SSW
Sbjct: 301 RAAEAVYSTEGKAQIKETINYYMSNAKIMKEGLEATGLKVYGGVNAPYLWVKTPNGLSSW 360

Query: 361 RFFDQMLYEANVVGTPGVGFGPSGEGYIRLTAFGERDDCIEAMRRIKNRL 410
           RFF+QMLYEANVVGTPGVGFGPSGEGYIRLTAFG+ +DC+EAMRRIKN L
Sbjct: 361 RFFEQMLYEANVVGTPGVGFGPSGEGYIRLTAFGDHNDCMEAMRRIKNWL 410


Lambda     K      H
   0.319    0.137    0.419 

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: 734
Number of extensions: 26
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: 410
Length of database: 410
Length adjustment: 31
Effective length of query: 379
Effective length of database: 379
Effective search space:   143641
Effective search space used:   143641
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 350075 BT0547 (aspartate aminotransferase (NCBI ptt file))
to HMM TIGR03542 (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/TIGR03542.hmm
# target sequence database:        /tmp/gapView.18122.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03542  [M=402]
Accession:   TIGR03542
Description: DAPAT_plant: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.9e-204  665.0   0.0   2.1e-204  664.8   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350075  BT0547 aspartate aminotransferas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350075  BT0547 aspartate aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.8   0.0  2.1e-204  2.1e-204       2     400 ..       3     408 ..       2     410 .] 0.99

  Alignments for each domain:
  == domain 1  score: 664.8 bits;  conditional E-value: 2.1e-204
                          TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrGyGpeqGl 77 
                                         vnehflkl++sylfs+iakkv++f+ ++p++diirlgiGdvtqPl+ka+iea+++aveelas++tfrGyGpeqG+
  lcl|FitnessBrowser__Btheta:350075   3 LVNEHFLKLPGSYLFSDIAKKVNTFKITHPKQDIIRLGIGDVTQPLPKACIEAMHKAVEELASKDTFRGYGPEQGY 78 
                                        58************************************************************************** PP

                          TIGR03542  78 dllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsavlaGragvld.ddgk 149
                                        d+l+eai+++++++r    +p+eif++dGak+d++++ +++++d++v+v+dP+yPvy+ds+v++Gragvl+  +gk
  lcl|FitnessBrowser__Btheta:350075  79 DFLIEAIIKNDFAPRgihFSPSEIFVNDGAKSDTGNIGDILRHDNSVGVTDPIYPVYIDSNVMCGRAGVLEeGTGK 154
                                        ***************9999***************************************************9679** PP

                          TIGR03542 150 ykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyakendslilfdaayeafisdpslP 225
                                        +++++y+pct+en+fiPe+p+++ +di+ylC+PnnPtGt+ltk +lk++vdya +nd+lilfdaayea+i+d ++P
  lcl|FitnessBrowser__Btheta:350075 155 WSNVTYMPCTSENDFIPEIPDKR-IDIVYLCYPNNPTGTTLTKPELKKWVDYALANDTLILFDAAYEAYIQDADVP 229
                                        **********************9.**************************************************** PP

                          TIGR03542 226 ksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....eslkklWerllctkfnGaslivqraaea 297
                                        +siyei+gak+caie+rsfskt+GftGvr+gytvvPkel++++      +l+klW+r++ctkfnG+s+i+qraaea
  lcl|FitnessBrowser__Btheta:350075 230 HSIYEIKGAKKCAIEFRSFSKTAGFTGVRCGYTVVPKELTAATLegdrIPLNKLWNRRQCTKFNGTSYITQRAAEA 305
                                        ****************************************9987777799************************** PP

                          TIGR03542 298 vlakeglqqikeaisyymenarilrkaleaaglkvyGGenaPylWvklpegissedffdkllkeaevvgtPGsGfG 373
                                        v++ eg+ qike+i+yym+na+i++++lea+glkvyGG+naPylWvk+p+g+ss++ff+++l+ea+vvgtPG+GfG
  lcl|FitnessBrowser__Btheta:350075 306 VYSTEGKAQIKETINYYMSNAKIMKEGLEATGLKVYGGVNAPYLWVKTPNGLSSWRFFEQMLYEANVVGTPGVGFG 381
                                        **************************************************************************** PP

                          TIGR03542 374 ssGeGfvrlsalgkredivealerike 400
                                        +sGeG++rl+a+g+++d++ea++rik+
  lcl|FitnessBrowser__Btheta:350075 382 PSGEGYIRLTAFGDHNDCMEAMRRIKN 408
                                        *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (410 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.03
//
[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