GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas simiae WCS417

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate GFF3433 PS417_17565 branched-chain amino acid aminotransferase

Query= reanno::pseudo5_N2C3_1:AO356_22970
         (339 letters)



>FitnessBrowser__WCS417:GFF3433
          Length = 339

 Score =  631 bits (1628), Expect = 0.0
 Identities = 302/339 (89%), Positives = 319/339 (94%)

Query: 1   MGNESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEG 60
           MGNESINWDKLGFDYIKTDKR+L  W++G W AGTLTDDNVLHISEGSTALHYGQQCFEG
Sbjct: 1   MGNESINWDKLGFDYIKTDKRFLQVWKNGEWQAGTLTDDNVLHISEGSTALHYGQQCFEG 60

Query: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGT 120
           LKAYRCKDGSINLFRPDQNAARMQRSCARLLMP V TE F++ACKQVV+ANE FIPPYG+
Sbjct: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTEVFIDACKQVVKANEHFIPPYGS 120

Query: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGT 180
           GGALYLRPFVIG GDNIGVRTAPEFIFS+FCIPVGAYFKGGL PHNF IS+FDRAAPQGT
Sbjct: 121 GGALYLRPFVIGTGDNIGVRTAPEFIFSVFCIPVGAYFKGGLVPHNFQISTFDRAAPQGT 180

Query: 181 GAAKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRS 240
           GAAKVGGNYAASLMPGS+AKK+ FAD IYLDPMTHSKIEEVGSANFFGITHDN F+TP+S
Sbjct: 181 GAAKVGGNYAASLMPGSEAKKSGFADAIYLDPMTHSKIEEVGSANFFGITHDNKFITPKS 240

Query: 241 PSVLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDK 300
           PSVLPGITRLSLIELAK+RLGLEV+EG+VFIDKL  FKEAGACGTAAVI+PIGGI Y  K
Sbjct: 241 PSVLPGITRLSLIELAKTRLGLEVVEGEVFIDKLDQFKEAGACGTAAVISPIGGIQYNGK 300

Query: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339
           LHVFHSETEVGPITQKLYKELTGVQTGDVEAP GWIVKV
Sbjct: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPQGWIVKV 339


Lambda     K      H
   0.320    0.138    0.422 

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: 535
Number of extensions: 10
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: 339
Length of database: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate GFF3433 PS417_17565 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01123.hmm
# target sequence database:        /tmp/gapView.5633.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-142  460.5   0.0   1.4e-142  460.3   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF3433  PS417_17565 branched-chain amino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3433  PS417_17565 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.3   0.0  1.4e-142  1.4e-142       1     313 []      31     339 .]      31     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: 460.3 bits;  conditional E-value: 1.4e-142
                           TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealk 75 
                                         W++++l+ ++ l+++egs++lhYgq++feGlkayR++dG+i+lfRpd+na+R++rs+ rll+P++++e+f++a+k
  lcl|FitnessBrowser__WCS417:GFF3433  31 WQAGTLTDDNVLHISEGSTALHYGQQCFEGLKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTEVFIDACK 105
                                         *************************************************************************** PP

                           TIGR01123  76 qlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkG 150
                                         q+vka+++++p+++s+ +LYlRPf+i+t+dn+Gv++a+e++f+v++ PvGaYfkggl p ++f  + ++Raap+G
  lcl|FitnessBrowser__WCS417:GFF3433 106 QVVKANEHFIPPYGSGGALYLRPFVIGTGDNIGVRTAPEFIFSVFCIPVGAYFKGGLVP-HNFQISTFDRAAPQG 179
                                         ***********************************************************.8998899******** PP

                           TIGR01123 151 tGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresll 225
                                         tGa+kvgGnYaasl++ ++a+++g++d++yldp+++ kieevG+an+f+it+d ++++tp+s+s+L+g+tr sl+
  lcl|FitnessBrowser__WCS417:GFF3433 180 TGAAKVGGNYAASLMPGSEAKKSGFADAIYLDPMTHSKIEEVGSANFFGITHD-NKFITPKSPSVLPGITRLSLI 253
                                         *****************************************************.********************* PP

                           TIGR01123 226 elakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkklrdeltdi 298
                                         elak  lglev e+e+ id+l++++eaG    acGtaavi+P+g+++ +gk ++++se evG++t+kl++elt++
  lcl|FitnessBrowser__WCS417:GFF3433 254 ELAKTrLGLEVVEGEVFIDKLDQFKEAG----ACGTAAVISPIGGIQYNGKLHVFHSEtEVGPITQKLYKELTGV 324
                                         ****99**********************....*************************99**************** PP

                           TIGR01123 299 qyGkledkegWivev 313
                                         q+G++e+++gWiv+v
  lcl|FitnessBrowser__WCS417:GFF3433 325 QTGDVEAPQGWIVKV 339
                                         *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (339 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: 00:00:00.00
# Mc/sec: 10.80
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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