Alignments for a candidate for ilvA in Oleispira antarctica

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Oleispira antarctica

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_084687629.1 OLEAN_RS17970 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000967895.1:WP_084687629.1
          Length = 519

 Score =  522 bits (1344), Expect = e-152
 Identities = 266/503 (52%), Positives = 362/503 (71%), Gaps = 5/503 (0%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +Y++ +L A VY+ A  +PL     LS RL N I VKRED+QPV+SFK+RGAY  +  LT
Sbjct: 16  QYIKKILSANVYDVAIESPLHIAPFLSERLGNNIWVKREDKQPVYSFKIRGAYNKVVQLT 75

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134
           +++KA GV+ ASAGNHAQG+A ++  LG+KA IVMP  T +IKV + +  G +V+LHG  
Sbjct: 76  DKEKAAGVVAASAGNHAQGLALAAKELGIKATIVMPLTTPEIKVKSCKARGAKVVLHGDT 135

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGGGLA 193
           FDEA A + +L +++G+T++ P+D P VIAGQGT+ +E+L+Q +  +D +FVPVGGGG+ 
Sbjct: 136 FDEAFAYSQKLVEEKGYTYIHPYDDPEVIAGQGTIGMEILRQLNDPIDAIFVPVGGGGII 195

Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253
           AG+A  +K L P+IK+I VE+ +SACL AAL AG  V LP VG+FA+GVAV +IG  T+ 
Sbjct: 196 AGIAAYVKFLRPEIKIIGVESTESACLHAALAAGRRVTLPSVGIFADGVAVAQIGKNTWD 255

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           + + Y+D++IT   D +CAA+KD+F+D RAV EP+GAL +AGMKKY+    I+G  L  I
Sbjct: 256 IARHYVDEVITCSPDELCAAIKDIFDDTRAVCEPAGALGVAGMKKYVEREGIKGANLVSI 315

Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373
           LSGANVNF  LRY+SE  E+GE REA+LAVTIPE  GSF +FC LLG R +TEFNYR+ D
Sbjct: 316 LSGANVNFDRLRYISEVAEIGEGREAILAVTIPERAGSFQQFCSLLGKRPITEFNYRYRD 375

Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGR-PSHPLQ 432
             +A I+VGV++    + R+++L  L    Y V+DL++DE++K H+R+MVGG  P     
Sbjct: 376 DNSAQIYVGVKVGAEKDARQKLLTELEAKDYPVLDLTEDEISKYHIRHMVGGHAPDSVND 435

Query: 433 ERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL---GDHEPDFE 489
           E LY FEFPE PGALL+FL +LG  +NISLFHYR+HG   GRVL   ++    + + + E
Sbjct: 436 ELLYRFEFPERPGALLQFLKSLGKKFNISLFHYRNHGAANGRVLVGLQVPKDKNQKKEVE 495

Query: 490 TRLNELGYDCHDETNNPAFRFFL 512
           T L ELGY   +ETNNPA++ FL
Sbjct: 496 TYLVELGYTYWNETNNPAYQLFL 518



 Score = 40.0 bits (92), Expect = 2e-07
 Identities = 23/84 (27%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 338 EALLAVTIPEEKGSFLKFCQLLGGR-SVTEFNYRFADAKNACIFVGVRLSRGLEERKEIL 396
           E L     PE  G+ L+F + LG + +++ F+YR   A N  + VG+++ +   ++KE+ 
Sbjct: 436 ELLYRFEFPERPGALLQFLKSLGKKFNISLFHYRNHGAANGRVLVGLQVPKDKNQKKEVE 495

Query: 397 QMLNDGGYSVVDLSDDEMAKLHVR 420
             L + GY+  + +++   +L +R
Sbjct: 496 TYLVELGYTYWNETNNPAYQLFLR 519


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: 700
Number of extensions: 48
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 514
Length of database: 519
Length adjustment: 35
Effective length of query: 479
Effective length of database: 484
Effective search space:   231836
Effective search space used:   231836
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_084687629.1 OLEAN_RS17970 (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.22406.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-239  780.9   0.1   2.8e-239  780.7   0.1    1.0  1  lcl|NCBI__GCF_000967895.1:WP_084687629.1  OLEAN_RS17970 threonine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000967895.1:WP_084687629.1  OLEAN_RS17970 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  780.7   0.1  2.8e-239  2.8e-239       1     499 []      16     518 ..      16     518 .. 0.98

  Alignments for each domain:
  == domain 1  score: 780.7 bits;  conditional E-value: 2.8e-239
                                 TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 
                                               +y+++il a+vy++a+e+pl+ a  lserl+n++++kred+qpv+sfk+rGaynk+ ql++++ka+Gv+
  lcl|NCBI__GCF_000967895.1:WP_084687629.1  16 QYIKKILSANVYDVAIESPLHIAPFLSERLGNNIWVKREDKQPVYSFKIRGAYNKVVQLTDKEKAAGVV 84 
                                               69******************************************************************* PP

                                 TIGR01124  70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekglt 138
                                               aasaGnhaqG+al+ak+lG+ka+ivmp ttpeikv+++ka+G++vvlhG+++dea a++++l +ekg t
  lcl|NCBI__GCF_000967895.1:WP_084687629.1  85 AASAGNHAQGLALAAKELGIKATIVMPLTTPEIKVKSCKARGAKVVLHGDTFDEAFAYSQKLVEEKGYT 153
                                               ********************************************************************* PP

                                 TIGR01124 139 fiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207
                                               +i+p+ddp viaGqGt+++e+lrq ++++da+fvpvGGGG+iaG+aa+vk l+peik+igve+++sa+l
  lcl|NCBI__GCF_000967895.1:WP_084687629.1 154 YIHPYDDPEVIAGQGTIGMEILRQLNDPIDAIFVPVGGGGIIAGIAAYVKFLRPEIKIIGVESTESACL 222
                                               ********************************************************************* PP

                                 TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaG 276
                                               ++al+aG+rv+l +vG+fadGvav ++G++t++++++y+d++++   de+caaikd+f+dtrav epaG
  lcl|NCBI__GCF_000967895.1:WP_084687629.1 223 HAALAAGRRVTLPSVGIFADGVAVAQIGKNTWDIARHYVDEVITCSPDELCAAIKDIFDDTRAVCEPAG 291
                                               ********************************************************************* PP

                                 TIGR01124 277 alalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvev 345
                                               al++aG+kkyv+++gi++ +lv+ilsGan+nfdrlry+se ae+Ge rea+lavtipe+ Gs+++f+++
  lcl|NCBI__GCF_000967895.1:WP_084687629.1 292 ALGVAGMKKYVEREGIKGANLVSILSGANVNFDRLRYISEVAEIGEGREAILAVTIPERAGSFQQFCSL 360
                                               ********************************************************************* PP

                                 TIGR01124 346 lGeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGra 413
                                               lG+r itefnyr+ dd++a+i+vGv++  e + r++ll++le ++y v+dlt+de++k h+r++vGG a
  lcl|NCBI__GCF_000967895.1:WP_084687629.1 361 LGKRPITEFNYRYRDDNSAQIYVGVKVGAEkDARQKLLTELEAKDYPVLDLTEDEISKYHIRHMVGGHA 429
                                               ***************************887256899*******************************97 PP

                                 TIGR01124 414 a.kvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpde..eaeefeqfl 479
                                                 +v++e ly+fefperpGall+fl++l +++nislfhyrnhGa+ Grvlvgl+vp++  +++e e+ l
  lcl|NCBI__GCF_000967895.1:WP_084687629.1 430 PdSVNDELLYRFEFPERPGALLQFLKSLGKKFNISLFHYRNHGAANGRVLVGLQVPKDknQKKEVETYL 498
                                               615666779**********************************************97511567899*** PP

                                 TIGR01124 480 aelgyryedetenpayrlfl 499
                                                elgy+y++et+npay+lfl
  lcl|NCBI__GCF_000967895.1:WP_084687629.1 499 VELGYTYWNETNNPAYQLFL 518
                                               *******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (519 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: 00:00:00.02
# Mc/sec: 10.00
//
[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