Alignments for a candidate for tdcB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Dechlorosoma suillum PS

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate Dsui_0728 Dsui_0728 threonine ammonia-lyase, biosynthetic, long form

Query= SwissProt::A0FKE6
         (606 letters)



>FitnessBrowser__PS:Dsui_0728
          Length = 503

 Score =  553 bits (1425), Expect = e-162
 Identities = 283/501 (56%), Positives = 365/501 (72%), Gaps = 2/501 (0%)

Query: 106 YEYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKL 165
           ++YLT IL+++VY+ A ETPL+ AP LS RLG   + KRED+QPVFSFK+RGAYN +A L
Sbjct: 3   HDYLTKILNARVYEAAVETPLELAPNLSHRLGNRFYFKREDMQPVFSFKLRGAYNKIAHL 62

Query: 166 PKEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGATVVLVGD 225
              QL++GVIC+SAGNHAQGVALSA ++GC AVIVMP TTP IK ++V   G  VVL G+
Sbjct: 63  TPAQLQRGVICASAGNHAQGVALSAAKIGCRAVIVMPTTTPQIKVQAVASRGGEVVLAGE 122

Query: 226 SYDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGGGL 285
           SYDEA A+A +  ++E  TF+ PFD P VI GQGT+GMEI RQ    IHA+FV +GGGGL
Sbjct: 123 SYDEAYAHAVELEKAEKLTFVHPFDDPYVIAGQGTIGMEILRQHGKPIHAVFVAIGGGGL 182

Query: 286 IAGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETY 345
            AG+AAY+K V P+IK+IGVE  DA+A+  S+  G+RV LD VG FADG AVK VGEET+
Sbjct: 183 AAGVAAYIKAVRPEIKVIGVETFDADAMKQSIAAGKRVRLDNVGLFADGTAVKFVGEETF 242

Query: 346 RLCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENVVA 405
           R+C E +D ++LV  DAICA+IKD+FE+ RSILEP+GALA+AGA+ Y K + LK +++VA
Sbjct: 243 RVCREYLDDIILVDTDAICAAIKDVFEDTRSILEPSGALAIAGAKEYAKQHKLKDKSLVA 302

Query: 406 ITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFKYRYN 465
           + SGAN NFDRLR V E A+VG QREAVLA  +PE PG++K+F  ++G  NITEF YR++
Sbjct: 303 VASGANTNFDRLRFVAERAEVGEQREAVLAVTLPEKPGAYKRFVSLIGSRNITEFNYRFH 362

Query: 466 SDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRT-NVHN 524
             +E A V   V +    E   +VE ++     T++LTD+++ K H+RH++GG    V N
Sbjct: 363 EARE-AHVFVGVQVANRAESTKLVESLKKHGYATLDLTDDEMGKLHVRHMVGGHAPQVEN 421

Query: 525 ELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEFEGR 584
           ELL RF FPE+PGALM FL+  S  WNISLFHYR  G     VLVG+QVPP E+ EF+  
Sbjct: 422 ELLYRFEFPERPGALMNFLNRMSSGWNISLFHYRNHGADYGRVLVGMQVPPAEMGEFQTF 481

Query: 585 ADSLGYEYAMESLNEAYQLIM 605
              LGY +  E+ N AY+L +
Sbjct: 482 LQELGYHHWDETANPAYKLFL 502


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: 697
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: 503
Length adjustment: 36
Effective length of query: 570
Effective length of database: 467
Effective search space:   266190
Effective search space used:   266190
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 Dsui_0728 Dsui_0728 (threonine ammonia-lyase, biosynthetic, long form)
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.11768.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-260  850.6   0.9   2.1e-260  850.4   0.9    1.0  1  lcl|FitnessBrowser__PS:Dsui_0728  Dsui_0728 threonine ammonia-lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0728  Dsui_0728 threonine ammonia-lyase, biosynthetic, long form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  850.4   0.9  2.1e-260  2.1e-260       1     499 []       4     502 ..       4     502 .. 1.00

  Alignments for each domain:
  == domain 1  score: 850.4 bits;  conditional E-value: 2.1e-260
                         TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnha 77 
                                       dyl++il+arvyeaavetple a +ls+rl+nr ++kred+qpvfsfklrGaynk+a+l++ q  +Gvi+asaGnha
  lcl|FitnessBrowser__PS:Dsui_0728   4 DYLTKILNARVYEAAVETPLELAPNLSHRLGNRFYFKREDMQPVFSFKLRGAYNKIAHLTPAQLQRGVICASAGNHA 80 
                                       89*************************************************************************** PP

                         TIGR01124  78 qGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGt 154
                                       qGvalsa+k+G++avivmp+ttp+ikv+av ++Ggevvl Ge+ydea+a+a+el++ + ltf++pfddp viaGqGt
  lcl|FitnessBrowser__PS:Dsui_0728  81 QGVALSAAKIGCRAVIVMPTTTPQIKVQAVASRGGEVVLAGESYDEAYAHAVELEKAEKLTFVHPFDDPYVIAGQGT 157
                                       ***************************************************************************** PP

                         TIGR01124 155 valellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvav 231
                                       +++e+lrq+ ++++avfv++GGGGl+aGvaa++k+++peikvigve+ d++a+kq+++aG+rv+ld+vGlfadG+av
  lcl|FitnessBrowser__PS:Dsui_0728 158 IGMEILRQHGKPIHAVFVAIGGGGLAAGVAAYIKAVRPEIKVIGVETFDADAMKQSIAAGKRVRLDNVGLFADGTAV 234
                                       ***************************************************************************** PP

                         TIGR01124 232 kevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnf 308
                                       k vG+etfr+c+eylddi+lvdtd++caaikdvfedtr++lep+Gala+aG k+y+++++++dk+lva++sGan nf
  lcl|FitnessBrowser__PS:Dsui_0728 235 KFVGEETFRVCREYLDDIILVDTDAICAAIKDVFEDTRSILEPSGALAIAGAKEYAKQHKLKDKSLVAVASGANTNF 311
                                       ***************************************************************************** PP

                         TIGR01124 309 drlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarl 385
                                       drlr+v+erae+Geqrea+lavt+pe++G++++fv+++G+r+itefnyr+ ++ +ah+fvGvq+a+++e ++l+++l
  lcl|FitnessBrowser__PS:Dsui_0728 312 DRLRFVAERAEVGEQREAVLAVTLPEKPGAYKRFVSLIGSRNITEFNYRFHEAREAHVFVGVQVANRAESTKLVESL 388
                                       ***************************************************************************** PP

                         TIGR01124 386 eeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvl 462
                                       +++gy+++dltdde+ klhvr++vGG a +vene ly+fefperpGal++fl+ + + wnislfhyrnhGadyGrvl
  lcl|FitnessBrowser__PS:Dsui_0728 389 KKHGYATLDLTDDEMGKLHVRHMVGGHAPQVENELLYRFEFPERPGALMNFLNRMSSGWNISLFHYRNHGADYGRVL 465
                                       ***************************************************************************** PP

                         TIGR01124 463 vglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                       vg++vp++e+ ef++fl+elgy+ +det npay+lfl
  lcl|FitnessBrowser__PS:Dsui_0728 466 VGMQVPPAEMGEFQTFLQELGYHHWDETANPAYKLFL 502
                                       ************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (503 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: 7.59
//
[ok]

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

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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

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