Alignments for a candidate for DAPtransferase in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Sedimenticola selenatireducens DSM 17993

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_029133026.1 A3GO_RS0108435 LL-diaminopimelate aminotransferase

Query= BRENDA::O26158
         (410 letters)



>NCBI__GCF_000428045.1:WP_029133026.1
          Length = 408

 Score =  537 bits (1384), Expect = e-157
 Identities = 259/409 (63%), Positives = 318/409 (77%), Gaps = 3/409 (0%)

Query: 1   MVTVNENYLLLKSSYIFSEINRRVEEFQRKNPDADIIRMGIGDVTRPLPEAVVEAFHRAV 60
           M+ +NENY  L++SY+FS I +RV  FQ+ N D  +I++GIGDVTR LP+A V+AFH AV
Sbjct: 1   MIKINENYQKLQASYLFSNIAKRVNAFQQSNQDKKLIKLGIGDVTRALPDACVKAFHLAV 60

Query: 61  DEMAEEETFRGYGPEQGYPFLREAIAENDYASRGVDITADEIFISDGAKCDTGNIQEIFG 120
           DEMA + TF GYGPEQGY FLREAIA+ND+ +RG  + ADE+F+SDGAKCD+GN QEIF 
Sbjct: 61  DEMANDATFHGYGPEQGYDFLREAIAKNDFQARGAQVDADEVFVSDGAKCDSGNFQEIFS 120

Query: 121 LDNVVAVTDPVYPVYVESNVMAGRAGPADDD-GRYSGLVYLPCTEENSFIPSLPEERVDL 179
            D  VA+ DPVYPVYV++NVMAGR+G  D + GRY  LVYL    +N FIP LP+  VDL
Sbjct: 121 TDITVAIPDPVYPVYVDTNVMAGRSGSWDAELGRYENLVYLDGNRDNGFIPDLPDRPVDL 180

Query: 180 IYLCYPNNPTGTTLTEKQLAEWVDYARDSGSLILFDAAYEAYIQEDGIPHSIYEVEGARE 239
           IYLC+PNNP G+T T +QL +WVDYA+ + SLILFDAAYEA++Q+  +P SIYEVEGARE
Sbjct: 181 IYLCFPNNPAGSTATREQLKQWVDYAKANKSLILFDAAYEAFVQDADLPRSIYEVEGARE 240

Query: 240 VAIEFRSFSKNAGFTGTRCAFTVVPEELEVPDSSGRMHSVRELWNRRQTTKFNGVSYPVQ 299
           VA+EFRSFSK AGFTGTRCA+TVVP+E      +G+  SV  LWNRR TTKFN VSYPVQ
Sbjct: 241 VAVEFRSFSKTAGFTGTRCAYTVVPKECMAYTEAGQAVSVHSLWNRRHTTKFNSVSYPVQ 300

Query: 300 RAAEAVYTPEGQREIRESIDYYMENARIIRESLERAGLRYYGGVNAPYIWIRTPEGMDSW 359
           RAAEAVY+ EGQ +I+E I YY+ NA+ IRE +E  G    GGVN+PYIWI +    DSW
Sbjct: 301 RAAEAVYSAEGQAQIKELIAYYLNNAKYIREKMEALGYECIGGVNSPYIWIDSK--CDSW 358

Query: 360 QFFDTLLNDAEVVGTPGSGFGPSGEGYFRLTAFNSFRNTVKAMERISEL 408
           +FFD LLN+A VV TPG+GFG  GEGY R++AFNS+ N  +AMERIS++
Sbjct: 359 EFFDRLLNEAAVVCTPGAGFGKCGEGYIRISAFNSYENVTEAMERISKI 407


Lambda     K      H
   0.317    0.136    0.403 

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: 569
Number of extensions: 21
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: 410
Length of database: 408
Length adjustment: 31
Effective length of query: 379
Effective length of database: 377
Effective search space:   142883
Effective search space used:   142883
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: 50 (23.9 bits)

Align candidate WP_029133026.1 A3GO_RS0108435 (LL-diaminopimelate aminotransferase)
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.18663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-180  586.0   0.4   2.1e-180  585.8   0.4    1.0  1  lcl|NCBI__GCF_000428045.1:WP_029133026.1  A3GO_RS0108435 LL-diaminopimelat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029133026.1  A3GO_RS0108435 LL-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.8   0.4  2.1e-180  2.1e-180       2     400 ..       3     406 ..       2     408 .] 0.98

  Alignments for each domain:
  == domain 1  score: 585.8 bits;  conditional E-value: 2.1e-180
                                 TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrG 70 
                                               k+ne+++kl++sylfs+iak+v+ f+++n ++++i+lgiGdvt+ l+ a+++a++ av+e+a++ tf G
  lcl|NCBI__GCF_000428045.1:WP_029133026.1   3 KINENYQKLQASYLFSNIAKRVNAFQQSNQDKKLIKLGIGDVTRALPDACVKAFHLAVDEMANDATFHG 71 
                                               89******************************************************************* PP

                                 TIGR03542  71 yGpeqGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsav 136
                                               yGpeqG+d+lreaia++++++r   +d++e+f+sdGakcd ++++e+f++d tva+ dPvyPvyvd++v
  lcl|NCBI__GCF_000428045.1:WP_029133026.1  72 YGPEQGYDFLREAIAKNDFQARgaqVDADEVFVSDGAKCDSGNFQEIFSTDITVAIPDPVYPVYVDTNV 140
                                               *********************9999******************************************** PP

                                 TIGR03542 137 laGragvld.ddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyake 204
                                               +aGr+g  d + g+y+++vyl   ++n+fiP+lp+++ vd+iylC+PnnP+G+++t+eqlk++vdyak+
  lcl|NCBI__GCF_000428045.1:WP_029133026.1 141 MAGRSGSWDaELGRYENLVYLDGNRDNGFIPDLPDRP-VDLIYLCFPNNPAGSTATREQLKQWVDYAKA 208
                                               *********899************************9.******************************* PP

                                 TIGR03542 205 ndslilfdaayeafisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg.... 269
                                               n+slilfdaayeaf++d +lP+siye+ega+e+a+e+rsfskt+GftG+r++ytvvPke ++ ++    
  lcl|NCBI__GCF_000428045.1:WP_029133026.1 209 NKSLILFDAAYEAFVQDADLPRSIYEVEGAREVAVEFRSFSKTAGFTGTRCAYTVVPKECMAYTEagqa 277
                                               ***********************************************************9876666777 PP

                                 TIGR03542 270 eslkklWerllctkfnGaslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGena 338
                                                s+++lW+r+ +tkfn +s++vqraaeav++ eg+ qike+i+yy++na+ +r+++ea g++  GG+n+
  lcl|NCBI__GCF_000428045.1:WP_029133026.1 278 VSVHSLWNRRHTTKFNSVSYPVQRAAEAVYSAEGQAQIKELIAYYLNNAKYIREKMEALGYECIGGVNS 346
                                               99******************************************************************* PP

                                 TIGR03542 339 PylWvklpegissedffdkllkeaevvgtPGsGfGssGeGfvrlsalgkredivealerike 400
                                               Py+W+   ++ +s++ffd+ll+ea vv tPG GfG++GeG++r+sa++++e+++ea+eri++
  lcl|NCBI__GCF_000428045.1:WP_029133026.1 347 PYIWID--SKCDSWEFFDRLLNEAAVVCTPGAGFGKCGEGYIRISAFNSYENVTEAMERISK 406
                                               ****86..567*************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (408 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: 10.70
//
[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