Alignments for a candidate for ilvA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Cupriavidus basilensis 4G11

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate RR42_RS02315 RR42_RS02315 threonine dehydratase

Query= SwissProt::A0FKE6
         (606 letters)



>FitnessBrowser__Cup4G11:RR42_RS02315
          Length = 508

 Score =  512 bits (1319), Expect = e-149
 Identities = 266/503 (52%), Positives = 354/503 (70%), Gaps = 5/503 (0%)

Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166
           +YL  IL++KVYDVA ET L  A  LS R G  VW KRED QPVFSFK+RGAYN MA L 
Sbjct: 6   DYLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLS 65

Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGAT---VVLV 223
            E+L++GVI +SAGNHAQGVALSA RL C A+I MPVTTP +K  +V+  G     +VL 
Sbjct: 66  PEELKRGVIAASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEWVEIVLH 125

Query: 224 GDSYDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGG 283
           GDSY +A  +A    +    TFI PFD P+VI GQGT+ MEI RQ    +HA+FV +GGG
Sbjct: 126 GDSYSDAYNHAAVLEKKHKLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGG 185

Query: 284 GLIAGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEE 343
           GLI+GIA+Y+K V P+IK+IGV+ +D++A+  S+  G+RV L +VG F+DG AVK+VG+E
Sbjct: 186 GLISGIASYIKAVRPEIKVIGVQTVDSDAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKE 245

Query: 344 TYRLCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENV 403
           T+R+  EL+D ++LV  DAICA +KD+F++ RSILEPAGA+A+AG + Y +   LKG+++
Sbjct: 246 TFRITRELVDEIILVDTDAICAGLKDVFQDTRSILEPAGAMAVAGLKLYAEREKLKGQHL 305

Query: 404 VAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFKYR 463
           VAI  GANMNFDRLR V E A+VG  REAV A  +PE+ GSFK+F E +G  N+TEF YR
Sbjct: 306 VAIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRFCEQLGTRNVTEFNYR 365

Query: 464 YNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTNV- 522
             +DK  A +   V + +  E E +          T++L++++L K H+R+++GG + + 
Sbjct: 366 I-ADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGGHSPLA 424

Query: 523 HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEFE 582
           H+ELL RF FPE+PGALM+FL + SP WNISLFHYR QG   +N+LVGIQVP +E   F 
Sbjct: 425 HDELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFR 484

Query: 583 GRADSLGYEYAMESLNEAYQLIM 605
               +LGY +  E+ N  Y+L +
Sbjct: 485 DFLATLGYVHWEETENPVYKLFL 507


Lambda     K      H
   0.318    0.136    0.393 

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: 704
Number of extensions: 31
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: 606
Length of database: 508
Length adjustment: 36
Effective length of query: 570
Effective length of database: 472
Effective search space:   269040
Effective search space used:   269040
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: 53 (25.0 bits)

Align candidate RR42_RS02315 RR42_RS02315 (threonine dehydratase)
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.27152.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-245  801.1   0.1   2.1e-245  800.9   0.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS02315  RR42_RS02315 threonine dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS02315  RR42_RS02315 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  800.9   0.1  2.1e-245  2.1e-245       1     499 []       6     507 ..       6     507 .. 0.99

  Alignments for each domain:
  == domain 1  score: 800.9 bits;  conditional E-value: 2.1e-245
                                 TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 
                                               dylr+il+a+vy++a+et l  a+ ls+r +n+v++kred qpvfsfklrGaynkma+ls+e+  +Gvi
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315   6 DYLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLSPEELKRGVI 74 
                                               89******************************************************************* PP

                                 TIGR01124  70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGge...vvlhGenydeakakalelaqek 135
                                               aasaGnhaqGvalsa++l +ka+i mp ttp++k+dav+++Gge   +vlhG++y++a+++a  l++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315  75 AASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEwveIVLHGDSYSDAYNHAAVLEKKH 143
                                               ******************************************9544489******************** PP

                                 TIGR01124 136 gltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaeds 204
                                                ltfi+pfddp viaGqGt+a+e+lrq+  +l+avfv++GGGGli+G+a+++k+++peikvigv++ ds
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315 144 KLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGGGLISGIASYIKAVRPEIKVIGVQTVDS 212
                                               ********************************************************************* PP

                                 TIGR01124 205 aalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravle 273
                                               +a+k++++aG+rv+l++vGlf+dG+avk vG+etfr+++e++d+i+lvdtd++ca +kdvf+dtr++le
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315 213 DAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKETFRITRELVDEIILVDTDAICAGLKDVFQDTRSILE 281
                                               ********************************************************************* PP

                                 TIGR01124 274 paGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkf 342
                                               paGa+a+aGlk y++++++++++lvai++Gan+nfdrlr+v+erae+Ge rea++av+ipee+Gs+++f
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315 282 PAGAMAVAGLKLYAEREKLKGQHLVAIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRF 350
                                               ********************************************************************* PP

                                 TIGR01124 343 vevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGG 411
                                               +e lG r++tefnyr+ad++ ahifvGvq+a+++e+++++a ++++g++++dl++delak h+ry+vGG
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315 351 CEQLGTRNVTEFNYRIADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGG 419
                                               ********************************************************************* PP

                                 TIGR01124 412 raakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqfla 480
                                                +  +++e ly+fefperpGal++fl+++ ++wnislfhyrn G+d  ++lvg++vp++e+ +f +fla
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315 420 HSPLAHDELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFRDFLA 488
                                               ********************************************************************* PP

                                 TIGR01124 481 elgyryedetenpayrlfl 499
                                               +lgy  ++etenp+y+lfl
  lcl|FitnessBrowser__Cup4G11:RR42_RS02315 489 TLGYVHWEETENPVYKLFL 507
                                               ******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (508 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: 7.93
//
[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