GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Herbaspirillum seropedicae SmR1

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate HSERO_RS00265 HSERO_RS00265 threonine dehydratase

Query= reanno::Korea:Ga0059261_3694
         (420 letters)



>FitnessBrowser__HerbieS:HSERO_RS00265
          Length = 401

 Score =  406 bits (1043), Expect = e-118
 Identities = 203/394 (51%), Positives = 275/394 (69%), Gaps = 1/394 (0%)

Query: 21  TLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTLLQL 80
           TL D++AAA R+ G ++ TP + S+TLS + GA V+LKFENLQFTA++KERGA N L+ +
Sbjct: 3   TLNDIEAAARRLQGQILETPCVESRTLSQIVGAQVFLKFENLQFTASFKERGACNKLVDV 62

Query: 81  D-DAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKVMQTESHGATIILEG 139
                 A+GV+A SAGNHAQG+AYH  RLG+P TIVMP+ TP VK+ +T   GA ++L G
Sbjct: 63  AASGGGARGVVAMSAGNHAQGVAYHAQRLGLPATIVMPRFTPGVKIERTRGFGANVVLHG 122

Query: 140 ETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAPAIDTLIVPIGGGGL 199
           +T + A  HA +L    G TFVHP+DD  IIAGQGTV LEM+   P +D L+V IGGGGL
Sbjct: 123 DTLEAARTHAYELAEKEGLTFVHPYDDEAIIAGQGTVALEMMKAVPDLDCLVVSIGGGGL 182

Query: 200 ISGALTVAKAADKPIEVVGVQAELFPSMFNRFTGAHEPIGGDTLAEGIAVKEPGGLTAQI 259
           ++G    A+A    IE+VGVQ   FP+M N   G   P+G  T+AEGIAV  PG LT  I
Sbjct: 183 LAGMAVAARAIKPEIEIVGVQTRRFPTMVNAVKGTEHPVGASTIAEGIAVGTPGTLTRAI 242

Query: 260 VEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQPERFRGKTVGVILTG 319
           +    DE++LV E  +E+AV +LL+IEKT+VEGAGAAGLAAL+  P+RFRGK VG++L+G
Sbjct: 243 IAREADELLLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALVRYPDRFRGKRVGLVLSG 302

Query: 320 GNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVARIFQEQTVNILELSHQRIFT 379
           GNID  LL  ++ R + R+GRLAR+++  +D PG L ++  I  E   N+ E+ HQR FT
Sbjct: 303 GNIDPLLLTAIIERGMVRAGRLARVKVSSRDVPGTLARITGIVAEAGANVDEVHHQRAFT 362

Query: 380 NLPAKGLSLDVECETRDRAHLERLISALQEAGYE 413
            L A+ + +++  +TR R HL +++ AL+ AG+E
Sbjct: 363 LLAAQNVDIELVLQTRGRPHLAQVLQALRAAGFE 396


Lambda     K      H
   0.319    0.135    0.374 

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: 438
Number of extensions: 16
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: 420
Length of database: 401
Length adjustment: 31
Effective length of query: 389
Effective length of database: 370
Effective search space:   143930
Effective search space used:   143930
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 HSERO_RS00265 HSERO_RS00265 (threonine dehydratase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.1022.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.7e-126  406.0   2.7   8.7e-126  405.8   2.7    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS00265  HSERO_RS00265 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS00265  HSERO_RS00265 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.8   2.7  8.7e-126  8.7e-126       1     378 [.      21     397 ..      21     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.8 bits;  conditional E-value: 8.7e-126
                                  TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklsee.ekkrGvvaasaGnhaqGvalaa 67 
                                                tp   s tls+i+ga+v+lk enlq t sfk rGa nk+  +++  +  rGvva saGnhaqGva+ a
  lcl|FitnessBrowser__HerbieS:HSERO_RS00265  21 TPCVESRTLSQIVGAQVFLKFENLQFTASFKERGACNKLVDVAASgGGARGVVAMSAGNHAQGVAYHA 88 
                                                78999**********************************9988762579******************* PP

                                  TIGR01127  68 kvfgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGq 135
                                                ++ g++a+ivmP+++p  k++ t+++Ga+v+LhG++++ a  +a elae+eg++fvh++dDe +iaGq
  lcl|FitnessBrowser__HerbieS:HSERO_RS00265  89 QRLGLPATIVMPRFTPGVKIERTRGFGANVVLHGDTLEAARTHAYELAEKEGLTFVHPYDDEAIIAGQ 156
                                                ******************************************************************** PP

                                  TIGR01127 136 GtlgleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikaves 203
                                                Gt++le+++ +pd+d ++v +GGGGL++G+a+a++ ++pe+ ++Gv+++  p++v+++k    ++   
  lcl|FitnessBrowser__HerbieS:HSERO_RS00265 157 GTVALEMMKAVPDLDCLVVSIGGGGLLAGMAVAARAIKPEIEIVGVQTRRFPTMVNAVKGT--EHPVG 222
                                                ********************************************************98754..44557 PP

                                  TIGR01127 204 vktiaDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvd 271
                                                 +tia+Giav +pg+lt  i+    De++ vde +i +a+l+Lle +k+++egaGa+g+aa++     
  lcl|FitnessBrowser__HerbieS:HSERO_RS00265 223 ASTIAEGIAVGTPGTLTRAIIAREADELLLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALVRYPDR 290
                                                89*************************************************************97777 PP

                                  TIGR01127 272 vkgkkvavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehd 339
                                                  gk+v++v+sGGnid+ ll+ iie+g+v+ gr++++++   D PG+L ++++++ae++an+ +++h+
  lcl|FitnessBrowser__HerbieS:HSERO_RS00265 291 FRGKRVGLVLSGGNIDPLLLTAIIERGMVRAGRLARVKVSSRDVPGTLARITGIVAEAGANVDEVHHQ 358
                                                ******************************************************************** PP

                                  TIGR01127 340 rlskeialgaakvelelevkgkehleellktlrdkgyev 378
                                                r  + +a     +el l+++g+ hl ++l+ lr+ g+e 
  lcl|FitnessBrowser__HerbieS:HSERO_RS00265 359 RAFTLLAAQNVDIELVLQTRGRPHLAQVLQALRAAGFEA 397
                                                *************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (401 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: 9.20
//
[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:

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