Alignments for a candidate for ilvA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Shewanella amazonensis SB2B

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 6939184 Sama_3278 threonine dehydratase (RefSeq)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__SB2B:6939184
          Length = 531

 Score =  604 bits (1557), Expect = e-177
 Identities = 308/506 (60%), Positives = 382/506 (75%), Gaps = 10/506 (1%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           YL+ +L + VY+ A+VTPL  M KLS+RL   I +KRED QPVHSFKLRGAY  ++ LT+
Sbjct: 24  YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQ 83

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
            +   GV+ ASAGNHAQGVA S++  G+ A+IVMPT T DIK+DAVR  GG VLLHG +F
Sbjct: 84  PECERGVVCASAGNHAQGVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESF 143

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAG 195
           D+A A A  L+Q +G  ++ PFD   VIAGQGT+A E+LQQ   L+ VFVPVGGGGL AG
Sbjct: 144 DQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTVAQEMLQQQRDLELVFVPVGGGGLVAG 203

Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255
           +A   K + P +K+I VE ED+ACLKAA+ AG PV L +VGLFA+GVAVKRIG E FR+ 
Sbjct: 204 IAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVKRIGAEPFRIA 263

Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIR-------GE 308
           + Y+D+++TV SD ICAA+KD+FED RA+AEP+GAL+LAG+KKY+A              
Sbjct: 264 KHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTTPALAEAGKPAR 323

Query: 309 RLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFN 368
           ++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE  GSFLKFC+LLG R++TEFN
Sbjct: 324 KVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFN 383

Query: 369 YRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPS 428
           YRF+   +A +F G+RLS G  E KEI+  L  GG+ V DLS DE AKLHVRYMVGG P+
Sbjct: 384 YRFSGRDSAVVFAGIRLSGGQSELKEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGHPT 443

Query: 429 HPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL--GDHEP 486
            PL ERL+SFEFPE PGALL+FL TLG+ WNISLFHYR+HG  +GRVLA FE+  GD+E 
Sbjct: 444 EPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHGAAFGRVLAGFEVPEGDNEA 503

Query: 487 DFETRLNELGYDCHDETNNPAFRFFL 512
            F   L ELG+   +ET++PA+R FL
Sbjct: 504 -FGRFLTELGFVWQEETHSPAYRLFL 528


Lambda     K      H
   0.321    0.138    0.403 

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: 746
Number of extensions: 30
Number of successful extensions: 5
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: 514
Length of database: 531
Length adjustment: 35
Effective length of query: 479
Effective length of database: 496
Effective search space:   237584
Effective search space used:   237584
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: 52 (24.6 bits)

Align candidate 6939184 Sama_3278 (threonine dehydratase (RefSeq))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (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/TIGR01124.hmm
# target sequence database:        /tmp/gapView.15738.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01124  [M=499]
Accession:   TIGR01124
Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-235  768.3   0.0   1.9e-235  768.1   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6939184  Sama_3278 threonine dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939184  Sama_3278 threonine dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.1   0.0  1.9e-235  1.9e-235       2     499 .]      24     528 ..      23     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 768.1 bits;  conditional E-value: 1.9e-235
                         TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaq 78 
                                       yl++il ++vy++a++tpl+++ kls+rl+ +++lkred+qpv+sfklrGayn+++ql++ +  +Gv++asaGnhaq
  lcl|FitnessBrowser__SB2B:6939184  24 YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQPECERGVVCASAGNHAQ 100
                                       89*************************************************************************** PP

                         TIGR01124  79 GvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtv 155
                                       Gvalsa+  G+ avivmp+ttp+ik+dav+ +Gg+v+lhGe++d+a+a+a++laq +g  +iapfdd+ viaGqGtv
  lcl|FitnessBrowser__SB2B:6939184 101 GVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESFDQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTV 177
                                       ***************************************************************************** PP

                         TIGR01124 156 alellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavk 232
                                       a e+l+q++ dl+ vfvpvGGGGl+aG+aa+ k+++p +k+igve+ed+a+lk+a++aGe+v+l+qvGlfadGvavk
  lcl|FitnessBrowser__SB2B:6939184 178 AQEMLQQQR-DLELVFVPVGGGGLVAGIAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVK 253
                                       *******99.9****************************************************************** PP

                         TIGR01124 233 evGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakk.......giedktlvails 302
                                       ++G+e fr++k+y+d++v+v +de+caa+kd+fedtra++epaGal+laGlkky+a+        g   ++++ails
  lcl|FitnessBrowser__SB2B:6939184 254 RIGAEPFRIAKHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTtpalaeaGKPARKVAAILS 330
                                       ******************************************************98752222111455789****** PP

                         TIGR01124 303 GanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eer 378
                                       Gan+nf++lryvser+elGeq+ea+lav +pe +Gs+lkf+e+lG+ra+tefnyr++ +++a +f G++l+   +e 
  lcl|FitnessBrowser__SB2B:6939184 331 GANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFNYRFSGRDSAVVFAGIRLSGGqSEL 407
                                       **********************************************************************9864899 PP

                         TIGR01124 379 kellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhG 455
                                       ke++a+l++ g++v dl+ de aklhvry+vGG +++   erl+sfefpe pGallkfl+tl ++wnislfhyrnhG
  lcl|FitnessBrowser__SB2B:6939184 408 KEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGHPTEPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHG 484
                                       ***************************************************************************** PP

                         TIGR01124 456 adyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                       a++Grvl+g+evp+ ++e+f  fl elg+  ++et++payrlfl
  lcl|FitnessBrowser__SB2B:6939184 485 AAFGRVLAGFEVPEGDNEAFGRFLTELGFVWQEETHSPAYRLFL 528
                                       *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (531 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03
# Mc/sec: 8.42
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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