Alignments for a candidate for ilvA in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Derxia gummosa DSM 723

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_028310639.1 H566_RS0105405 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000482785.1:WP_028310639.1
          Length = 506

 Score =  516 bits (1328), Expect = e-151
 Identities = 271/503 (53%), Positives = 346/503 (68%), Gaps = 6/503 (1%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +YLR +L A VY+ A  T L     +S R+ N +L+KRED QPV SFKLRGAY  MA  T
Sbjct: 4   DYLRKILTARVYDVANETQLDAAPGISQRIGNRVLLKREDLQPVFSFKLRGAYNKMAHCT 63

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131
            EQ   GVI ASAGNHAQGVA  +ARLG KA+IVMPT T  +KVDAVR  GG   +++LH
Sbjct: 64  PEQLERGVIAASAGNHAQGVALGAARLGCKAVIVMPTTTPQVKVDAVRAHGGKSVQIVLH 123

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGG 190
           G ++ +A   A EL +Q G+T++ PFD P VIAGQGT+A+E+L+Q  A +  VFV +GGG
Sbjct: 124 GTSYSDAALHASELEKQHGYTFIHPFDDPYVIAGQGTVAMEILRQHQAPIHAVFVAIGGG 183

Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250
           GL +GVA  IKQ+ P IKVI V+  DS  +  ++ AG  V L  VGLF++G AVK +G E
Sbjct: 184 GLISGVAAYIKQVRPDIKVIGVQTVDSDAMTRSVKAGKRVTLADVGLFSDGTAVKLVGKE 243

Query: 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310
           TFRLC+E +DD +  D+D +CAA+KD+F D R+V EP+GALALAG+KKY   H ++ E L
Sbjct: 244 TFRLCRELVDDYVLCDTDEVCAAIKDVFMDTRSVVEPAGALALAGLKKYAKAHGLKDETL 303

Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370
             I  GAN+NF  LR+V+ER E+GE REAL AV+IPEE+GSF +FC+L+G RSVTEFNYR
Sbjct: 304 VAIACGANMNFARLRFVAERTEIGEAREALFAVSIPEERGSFKRFCELVGTRSVTEFNYR 363

Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430
            +D K A +FVG+  +   E  K I       GY+ VDLS DEMA  H+R+MVGG+ +  
Sbjct: 364 ISDEKTAHVFVGMSTANAGENEK-IAANFAKHGYATVDLSHDEMAADHIRHMVGGKSALA 422

Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFE 489
             E +YSF FPE PGAL+ FL ++   WNIS+FHYR+ G DY RVL   ++   E   F+
Sbjct: 423 AGELIYSFVFPERPGALMNFLTSMAPGWNISMFHYRNQGADYSRVLVGLQVPKGERKAFK 482

Query: 490 TRLNELGYDCHDETNNPAFRFFL 512
             L  LGY   DET NPA+R FL
Sbjct: 483 AFLAGLGYPYSDETENPAYRLFL 505


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: 667
Number of extensions: 36
Number of successful extensions: 9
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: 506
Length adjustment: 34
Effective length of query: 480
Effective length of database: 472
Effective search space:   226560
Effective search space used:   226560
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 WP_028310639.1 H566_RS0105405 (threonine ammonia-lyase, biosynthetic)
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.31571.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-248  809.7   1.4   5.3e-248  809.5   1.4    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028310639.1  H566_RS0105405 threonine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028310639.1  H566_RS0105405 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.5   1.4  5.3e-248  5.3e-248       1     499 []       4     505 ..       4     505 .. 0.99

  Alignments for each domain:
  == domain 1  score: 809.5 bits;  conditional E-value: 5.3e-248
                                 TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 
                                               dylr+il+arvy++a et l+ a  +s+r++nrvllkredlqpvfsfklrGaynkma+ ++eq  +Gvi
  lcl|NCBI__GCF_000482785.1:WP_028310639.1   4 DYLRKILTARVYDVANETQLDAAPGISQRIGNRVLLKREDLQPVFSFKLRGAYNKMAHCTPEQLERGVI 72 
                                               89******************************************************************* PP

                                 TIGR01124  70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakalelaqek 135
                                               aasaGnhaqGval+a++lG+kavivmp+ttp++kvdav+a+Gg   ++vlhG++y++a+ +a el++++
  lcl|NCBI__GCF_000482785.1:WP_028310639.1  73 AASAGNHAQGVALGAARLGCKAVIVMPTTTPQVKVDAVRAHGGksvQIVLHGTSYSDAALHASELEKQH 141
                                               ******************************************9444589******************** PP

                                 TIGR01124 136 gltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaeds 204
                                               g tfi+pfddp viaGqGtva+e+lrq++ +++avfv++GGGGli+Gvaa++kq++p+ikvigv++ ds
  lcl|NCBI__GCF_000482785.1:WP_028310639.1 142 GYTFIHPFDDPYVIAGQGTVAMEILRQHQAPIHAVFVAIGGGGLISGVAAYIKQVRPDIKVIGVQTVDS 210
                                               ********************************************************************* PP

                                 TIGR01124 205 aalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravle 273
                                               +a++++++aG+rv+l +vGlf+dG+avk vG+etfrlc+e++dd vl dtdevcaaikdvf dtr+v+e
  lcl|NCBI__GCF_000482785.1:WP_028310639.1 211 DAMTRSVKAGKRVTLADVGLFSDGTAVKLVGKETFRLCRELVDDYVLCDTDEVCAAIKDVFMDTRSVVE 279
                                               ********************************************************************* PP

                                 TIGR01124 274 paGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkf 342
                                               paGalalaGlkky++ +g++d+tlvai++Gan+nf rlr+v+er+e+Ge real+av+ipee+Gs+++f
  lcl|NCBI__GCF_000482785.1:WP_028310639.1 280 PAGALALAGLKKYAKAHGLKDETLVAIACGANMNFARLRFVAERTEIGEAREALFAVSIPEERGSFKRF 348
                                               ********************************************************************* PP

                                 TIGR01124 343 vevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGG 411
                                               +e++G r++tefnyr++d+++ah+fvG+ +a+  e+++++a++ ++gy++vdl++de+a  h+r++vGG
  lcl|NCBI__GCF_000482785.1:WP_028310639.1 349 CELVGTRSVTEFNYRISDEKTAHVFVGMSTANAGENEKIAANFAKHGYATVDLSHDEMAADHIRHMVGG 417
                                               ********************************************************************* PP

                                 TIGR01124 412 raakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqfla 480
                                               ++a +  e +ysf fperpGal++fl+++ + wnis+fhyrn Gady rvlvgl+vp+ e ++f+ fla
  lcl|NCBI__GCF_000482785.1:WP_028310639.1 418 KSALAAGELIYSFVFPERPGALMNFLTSMAPGWNISMFHYRNQGADYSRVLVGLQVPKGERKAFKAFLA 486
                                               ********************************************************************* PP

                                 TIGR01124 481 elgyryedetenpayrlfl 499
                                                lgy y detenpayrlfl
  lcl|NCBI__GCF_000482785.1:WP_028310639.1 487 GLGYPYSDETENPAYRLFL 505
                                               ******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (506 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.90
//
[ok]

This GapMind analysis is from Apr 10 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