Alignments for a candidate for tdcB in Duganella sacchari Sac-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Duganella sacchari Sac-22

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate WP_072786890.1 BUA36_RS18985 threonine ammonia-lyase, biosynthetic

Query= SwissProt::A0FKE6
         (606 letters)



>NCBI__GCF_900143065.1:WP_072786890.1
          Length = 511

 Score =  527 bits (1358), Expect = e-154
 Identities = 276/508 (54%), Positives = 360/508 (70%), Gaps = 10/508 (1%)

Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166
           +YL  +L+++VYDVA ETPL+ AP LS+R    ++ KRED+Q VFSFKIRGAYN MA L 
Sbjct: 4   DYLKKVLTARVYDVADETPLELAPTLSQRFENRIYFKREDMQGVFSFKIRGAYNKMAHLS 63

Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGAT---VVLV 223
             Q ++GVIC+SAGNHAQGVALSA R+GC AVIVMP TTP +K  +VK  G     VVL 
Sbjct: 64  DAQRKRGVICASAGNHAQGVALSAARMGCRAVIVMPTTTPQVKVDAVKARGGADVEVVLH 123

Query: 224 GDSYDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGG 283
           G+SY +A  +A    + +  TF+ PFD PDVI GQGT+GMEI RQ    IHAIFVP+GGG
Sbjct: 124 GESYTDAYNHALTLEKEQKLTFVHPFDDPDVIAGQGTIGMEILRQHSGPIHAIFVPIGGG 183

Query: 284 GLIAGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEE 343
           GLIAGIAAY+K++ PDIKIIGV+ LD++A+A SL  G+RV L  VG FADG AV++ GEE
Sbjct: 184 GLIAGIAAYVKQIRPDIKIIGVQSLDSDAMARSLKAGERVTLSDVGLFADGTAVRLAGEE 243

Query: 344 TYRLCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGL----- 398
           T+RL +E +D ++LV  DAI A+IKD+F + RSILEP+GAL++AGA+AY +   L     
Sbjct: 244 TFRLVQEYVDDIILVDTDAISAAIKDVFSDTRSILEPSGALSIAGAKAYIERAALTKDPI 303

Query: 399 KGENVVAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNIT 458
           K E ++ I SGANMNFDRLR V E A++G  REA+ A  +PE  GSFK+  ++VG  N+T
Sbjct: 304 KNETLITIASGANMNFDRLRFVAERAELGEAREALFAVTLPEQRGSFKRLCKLVGARNVT 363

Query: 459 EFKYRYNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGG 518
           EF YR  SDK+ A V   V +    E   +  R E    + ++LT ++L K HLRHL+GG
Sbjct: 364 EFTYRI-SDKDDAHVFCGVQIADRNESGALARRFEEHGFKALDLTHDELAKTHLRHLVGG 422

Query: 519 RTNV-HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDE 577
           ++ +  NELL RF FPE+PGALM+FLD+ +P WNISL HYR+QG     +++G+QVPP+E
Sbjct: 423 KSALADNELLYRFEFPERPGALMRFLDSMAPNWNISLCHYRSQGGDVGRIVIGLQVPPEE 482

Query: 578 VVEFEGRADSLGYEYAMESLNEAYQLIM 605
           + +F     +LGY Y  ES N  Y+L +
Sbjct: 483 MSDFAQFLATLGYRYWDESSNPVYKLFL 510


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: 698
Number of extensions: 33
Number of successful extensions: 6
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: 511
Length adjustment: 36
Effective length of query: 570
Effective length of database: 475
Effective search space:   270750
Effective search space used:   270750
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 WP_072786890.1 BUA36_RS18985 (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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.520691.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.9e-246  802.1   0.0     1e-245  802.0   0.0    1.0  1  NCBI__GCF_900143065.1:WP_072786890.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900143065.1:WP_072786890.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  802.0   0.0    1e-245    1e-245       1     499 []       4     510 ..       4     510 .. 0.98

  Alignments for each domain:
  == domain 1  score: 802.0 bits;  conditional E-value: 1e-245
                             TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasa 73 
                                           dyl+++l+arvy++a etple a +ls+r +nr+++kred+q vfsfk+rGaynkma+ls+ q+ +Gvi+asa
  NCBI__GCF_900143065.1:WP_072786890.1   4 DYLKKVLTARVYDVADETPLELAPTLSQRFENRIYFKREDMQGVFSFKIRGAYNKMAHLSDAQRKRGVICASA 76 
                                           89*********************************************************************** PP

                             TIGR01124  74 GnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakalelaqekgltfiapf 143
                                           GnhaqGvalsa+++G++avivmp+ttp++kvdavka+Gg   evvlhGe+y +a+++al l++e+ ltf++pf
  NCBI__GCF_900143065.1:WP_072786890.1  77 GNHAQGVALSAARMGCRAVIVMPTTTPQVKVDAVKARGGadvEVVLHGESYTDAYNHALTLEKEQKLTFVHPF 149
                                           **************************************86667****************************** PP

                             TIGR01124 144 ddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGer 216
                                           ddp+viaGqGt+++e+lrq++ +++a+fvp+GGGGliaG+aa+vkq++p+ik+igv++ ds+a++++l+aGer
  NCBI__GCF_900143065.1:WP_072786890.1 150 DDPDVIAGQGTIGMEILRQHSGPIHAIFVPIGGGGLIAGIAAYVKQIRPDIKIIGVQSLDSDAMARSLKAGER 222
                                           ************************************************************************* PP

                             TIGR01124 217 vkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvak 289
                                           v+l++vGlfadG+av+  G+etfrl++ey+ddi+lvdtd++ aaikdvf dtr++lep+Gal++aG k+y+++
  NCBI__GCF_900143065.1:WP_072786890.1 223 VTLSDVGLFADGTAVRLAGEETFRLVQEYVDDIILVDTDAISAAIKDVFSDTRSILEPSGALSIAGAKAYIER 295
                                           **********************************************************************986 PP

                             TIGR01124 290 .....kgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyr 357
                                                + i+++tl++i+sGan+nfdrlr+v+eraelGe real+avt+pe++Gs++++++++G r++tef+yr
  NCBI__GCF_900143065.1:WP_072786890.1 296 aaltkDPIKNETLITIASGANMNFDRLRFVAERAELGEAREALFAVTLPEQRGSFKRLCKLVGARNVTEFTYR 368
                                           2222156899*************************************************************** PP

                             TIGR01124 358 laddekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperp 430
                                           ++d+++ah+f Gvq+a+++e   l++r+ee+g+k +dlt+delak+h+r+lvGG++a ++ne ly+fefperp
  NCBI__GCF_900143065.1:WP_072786890.1 369 ISDKDDAHVFCGVQIADRNESGALARRFEEHGFKALDLTHDELAKTHLRHLVGGKSALADNELLYRFEFPERP 441
                                           ************************************************************************* PP

                             TIGR01124 431 GallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                           Gal++fl+++ ++wnisl hyr+ G+d Gr+++gl+vp+ee+++f qfla+lgyry+de++np+y+lfl
  NCBI__GCF_900143065.1:WP_072786890.1 442 GALMRFLDSMAPNWNISLCHYRSQGGDVGRIVIGLQVPPEEMSDFAQFLATLGYRYWDESSNPVYKLFL 510
                                           ********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (511 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: 00:00:00.00
# Mc/sec: 31.43
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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

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 catabolism of small carbon sources