Alignments for a candidate for ilvA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Pedobacter sp. GW460-11-11-14-LB5

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate CA265_RS15860 CA265_RS15860 threonine dehydratase

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



>FitnessBrowser__Pedo557:CA265_RS15860
          Length = 416

 Score =  825 bits (2132), Expect = 0.0
 Identities = 416/416 (100%), Positives = 416/416 (100%)

Query: 1   MNTTTPNTLDFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAY 60
           MNTTTPNTLDFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAY
Sbjct: 1   MNTTTPNTLDFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAY 60

Query: 61  NKISSLPQDALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGD 120
           NKISSLPQDALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGD
Sbjct: 61  NKISSLPQDALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGD 120

Query: 121 NVEVVLVGDTFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIV 180
           NVEVVLVGDTFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIV
Sbjct: 121 NVEVVLVGDTFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIV 180

Query: 181 MPVGGGGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAV 240
           MPVGGGGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAV
Sbjct: 181 MPVGGGGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAV 240

Query: 241 KRIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQIT 300
           KRIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQIT
Sbjct: 241 KRIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQIT 300

Query: 301 GKTVVCIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDI 360
           GKTVVCIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDI
Sbjct: 301 GKTVVCIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDI 360

Query: 361 TRFEFIKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416
           TRFEFIKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV
Sbjct: 361 TRFEFIKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416


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: 756
Number of extensions: 17
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: 416
Length of database: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
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 CA265_RS15860 CA265_RS15860 (threonine dehydratase)
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.15721.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.3e-193  629.3   0.3   1.5e-193  629.1   0.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15860  CA265_RS15860 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15860  CA265_RS15860 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.1   0.3  1.5e-193  1.5e-193       3     410 .]      11     416 .]       9     416 .] 0.99

  Alignments for each domain:
  == domain 1  score: 629.1 bits;  conditional E-value: 1.5e-193
                                  TIGR02079   3 iekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvca 70 
                                                 + a +rlk vvk+tPl+ n+ ls++y+a+iylkredlq+vrsyklrGaynk+++l ++ l +gvvca
  lcl|FitnessBrowser__Pedo557:CA265_RS15860  11 FQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQDALINGVVCA 78 
                                                57899*************************************************************** PP

                                  TIGR02079  71 saGnhaqGvayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekeg 138
                                                saGnhaqGvay+c+klg+kg++fmP  tPkqkv+++ +fGg+++ev+lvGdtfd++  +a    +++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS15860  79 SAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGDTFDDCLKEALAYSAEKS 146
                                                ******************************************************************** PP

                                  TIGR02079 139 ktlipPfddkdiieGqgtvaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeG 206
                                                +t+ipPfdd+++ieGq+tv+vei e+l++   d++++pvGGGGl+sGv++y+k+  ++ k++gveP G
  lcl|FitnessBrowser__Pedo557:CA265_RS15860 147 ATFIPPFDDEKVIEGQATVGVEIYEDLPD--LDMIVMPVGGGGLASGVSAYMKTVKPEVKLVGVEPLG 212
                                                *****************************..6************************************ PP

                                  TIGR02079 207 apslkaslkagevvtldkidkfvdGaavkrvGdlnfkalkkvvdevtlveegavcstildlynkegiv 274
                                                aps+ ++++ g + tl++id+fvdGaavkr+G+++++ +k+++d++ l++eg++c+til+lyn+++iv
  lcl|FitnessBrowser__Pedo557:CA265_RS15860 213 APSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIV 280
                                                ******************************************************************** PP

                                  TIGR02079 275 aePaGalsiaaleelseeikgktvvcvvsGgnndierleeikersllyeGlkhyflvkfpqraGalre 342
                                                +ePaGals+aal++l+++i+gktvvc+vsGgnndier++eike+sll+eGlkhyf+v+fpqr+Gal+ 
  lcl|FitnessBrowser__Pedo557:CA265_RS15860 281 VEPAGALSVAALDQLKDQITGKTVVCIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKL 348
                                                ******************************************************************** PP

                                  TIGR02079 343 flndvlGPndditkfeyvkksnretGevliGielsdkedfeGllerlkaadieyeainenetlyellv 410
                                                f+n+vlGP+ddit+fe++kk+n+e+G++l+Giels+k+d++ ll+r+k ++ e+ ++n+++tl+e+lv
  lcl|FitnessBrowser__Pedo557:CA265_RS15860 349 FVNEVLGPQDDITRFEFIKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416
                                                ******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (410 nodes)
Target sequences:                          1  (416 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: 9.26
//
[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