GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Enterococcus termitis LMG 8895

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate WP_069663723.1 BCR25_RS11385 threonine ammonia-lyase IlvA

Query= reanno::Pedo557:CA265_RS15860
         (416 letters)



>NCBI__GCF_001730305.1:WP_069663723.1
          Length = 418

 Score =  448 bits (1152), Expect = e-130
 Identities = 216/411 (52%), Positives = 294/411 (71%), Gaps = 4/411 (0%)

Query: 10  DFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQD 69
           D + A   LK VV +TPL+++  LS  Y  N+YLKREDLQ VRS+KLRGAY  I   P +
Sbjct: 8   DVEQAYATLKKVVTKTPLQYDMYLSQKYQCNVYLKREDLQKVRSFKLRGAYYAIKQTPHE 67

Query: 70  ALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGD 129
            L NGVVCASAGNHAQGVA++C ++ +   IFMP  TP+QK+ Q   FGGD V V L+GD
Sbjct: 68  VLKNGVVCASAGNHAQGVAFTCHEMNVAATIFMPTTTPQQKISQVKFFGGDEVTVQLIGD 127

Query: 130 TFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPD----LDMIVMPVGG 185
           TFD   K A  Y+      FI PF+D  ++ GQ TV VE++++  +    +D ++  +GG
Sbjct: 128 TFDASAKAAKEYAEIHHQAFIDPFNDLNIMAGQGTVAVEVFQEAQESEFQVDYLLAAIGG 187

Query: 186 GGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGH 245
           GGL SGVS Y K++ P   ++GVEPLGA SM  A + G P  L+ +++FVDGAAVK++G+
Sbjct: 188 GGLVSGVSTYTKSISPTTAVIGVEPLGAQSMRAAFDEGRPVMLDSVEKFVDGAAVKQVGN 247

Query: 246 ITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQITGKTVV 305
           +TYE     +D++  + EG++C+TIL+LY + AIVVEPAGALSV+AL+ +KD+I GK VV
Sbjct: 248 LTYEQTLAYVDELLAVDEGQVCSTILELYTKQAIVVEPAGALSVSALELMKDEIRGKNVV 307

Query: 306 CIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDITRFEF 365
           CI+SGGNNDI RM+EI+E+SL+FEGLKHYF++ FPQRPGAL+ FV ++LGP DDITRFE+
Sbjct: 308 CIISGGNNDINRMEEIEERSLIFEGLKHYFVINFPQRPGALREFVTDILGPDDDITRFEY 367

Query: 366 IKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416
            KK N+  GP ++GI L NK +  +LL +M  F  + I+L+ + +L+  LV
Sbjct: 368 TKKVNRGTGPVVLGILLKNKEELPNLLDKMAQFDPKYIDLSDNPSLYALLV 418


Lambda     K      H
   0.318    0.138    0.392 

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: 472
Number of extensions: 17
Number of successful extensions: 2
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: 416
Length of database: 418
Length adjustment: 31
Effective length of query: 385
Effective length of database: 387
Effective search space:   148995
Effective search space used:   148995
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_069663723.1 BCR25_RS11385 (threonine ammonia-lyase IlvA)
to HMM TIGR02079 (ilvA: threonine dehydratase (EC 4.3.1.19))

# 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/TIGR02079.hmm
# target sequence database:        /tmp/gapView.160115.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02079  [M=410]
Accession:   TIGR02079
Description: THD1: threonine dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-191  622.8   1.2   1.4e-191  622.6   1.2    1.0  1  NCBI__GCF_001730305.1:WP_069663723.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069663723.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  622.6   1.2  1.4e-191  1.4e-191       2     410 .]       8     418 .]       7     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 622.6 bits;  conditional E-value: 1.4e-191
                             TIGR02079   2 diekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvcasaGn 74 
                                           d+e+a+ +lk+vv++tPlq++ +ls+ky++++ylkredlq+vrs+klrGay+++kq  +e l++gvvcasaGn
  NCBI__GCF_001730305.1:WP_069663723.1   8 DVEQAYATLKKVVTKTPLQYDMYLSQKYQCNVYLKREDLQKVRSFKLRGAYYAIKQTPHEVLKNGVVCASAGN 80 
                                           89*********************************************************************** PP

                             TIGR02079  75 haqGvayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfdd 147
                                           haqGva++c++++v +t+fmP+ttP+qk+++vk+fGg+ + v l+Gdtfd++a aak+ +e +++ +i Pf+d
  NCBI__GCF_001730305.1:WP_069663723.1  81 HAQGVAFTCHEMNVAATIFMPTTTPQQKISQVKFFGGDEVTVQLIGDTFDASAKAAKEYAEIHHQAFIDPFND 153
                                           ************************************************************************* PP

                             TIGR02079 148 kdiieGqgtvaveileqleee..kidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkage 218
                                            +i++Gqgtvave++++ +e+  ++d++l+++GGGGl+sGv++y k++s++t++igveP Ga s++a++ +g+
  NCBI__GCF_001730305.1:WP_069663723.1 154 LNIMAGQGTVAVEVFQEAQESefQVDYLLAAIGGGGLVSGVSTYTKSISPTTAVIGVEPLGAQSMRAAFDEGR 226
                                           ****************9999889************************************************** PP

                             TIGR02079 219 vvtldkidkfvdGaavkrvGdlnfkalkkvvdevtlveegavcstildlynkegivaePaGalsiaaleelse 291
                                           +v ld ++kfvdGaavk+vG+l+++++ + vde+ +v+eg+vcstil+ly+k++iv+ePaGals++ale +++
  NCBI__GCF_001730305.1:WP_069663723.1 227 PVMLDSVEKFVDGAAVKQVGNLTYEQTLAYVDELLAVDEGQVCSTILELYTKQAIVVEPAGALSVSALELMKD 299
                                           ************************************************************************* PP

                             TIGR02079 292 eikgktvvcvvsGgnndierleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksn 364
                                           ei+gk+vvc++sGgnndi+r+eei+ersl++eGlkhyf+++fpqr+Galref+ d+lGP+ddit+fey+kk+n
  NCBI__GCF_001730305.1:WP_069663723.1 300 EIRGKNVVCIISGGNNDINRMEEIEERSLIFEGLKHYFVINFPQRPGALREFVTDILGPDDDITRFEYTKKVN 372
                                           ************************************************************************* PP

                             TIGR02079 365 retGevliGielsdkedfeGllerlkaadieyeainenetlyellv 410
                                           r+tG+v++Gi l++ke++  ll++++++d +y ++ +n  ly llv
  NCBI__GCF_001730305.1:WP_069663723.1 373 RGTGPVVLGILLKNKEELPNLLDKMAQFDPKYIDLSDNPSLYALLV 418
                                           *******************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (410 nodes)
Target sequences:                          1  (418 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: 15.36
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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