Alignments for a candidate for ilvA in Herbaspirillum seropedicae SmR1

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.19819.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: 9.88
//
[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