Alignments for a candidate for tdcB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Caulobacter crescentus NA1000

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate CCNA_03750 CCNA_03750 threonine dehydratase

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__Caulo:CCNA_03750
          Length = 400

 Score =  291 bits (744), Expect = 3e-83
 Identities = 170/395 (43%), Positives = 238/395 (60%), Gaps = 2/395 (0%)

Query: 2   LPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTS 61
           L    IQ A  RL+ ++ RT   HS   S+  G  ++ K ENLQ T A+K RGALN +  
Sbjct: 3   LDLAAIQAAAGRLQGQIERTPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKLML 62

Query: 62  QPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTG 121
                  +GVI ASAGNHAQG+A+    LGVP T+ MP++TP  KV  TRD+GA VV+ G
Sbjct: 63  LSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIVMPKTTPFVKVQHTRDFGATVVIEG 122

Query: 122 RNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGL 181
             +D+A A A + ++E+G  FVHPFDD  +MAGQGTI LE+L++ PD+  + VPIGGGGL
Sbjct: 123 ETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPVPIGGGGL 182

Query: 182 IAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTF 241
           I+G+ATA +   P +RIIG E A  PS  ++ +   +       T+A+G+AVK+ G  T+
Sbjct: 183 ISGVATAAKALKPDIRIIGCEPAMYPS--FTAKMRGVAAHCGGQTIAEGVAVKQVGELTY 240

Query: 242 PIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVL 301
            ++R L+D+V+L+EE  +  A+       K + EGAGA  LAALL         K   +L
Sbjct: 241 GVVRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLIL 300

Query: 302 SGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDRR 361
            GGNID + ++ V+ R LV A R   L++  DD PG L+ +A+ I    ANI  + H+R 
Sbjct: 301 CGGNIDTRLLASVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRL 360

Query: 362 SKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGY 396
           +  +P    E  I +ETR  +H QEV+  L+  GY
Sbjct: 361 ALDVPAKGAEFDITIETRDAQHTQEVMEALRESGY 395


Lambda     K      H
   0.319    0.137    0.383 

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: 371
Number of extensions: 13
Number of successful extensions: 3
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: 402
Length of database: 400
Length adjustment: 31
Effective length of query: 371
Effective length of database: 369
Effective search space:   136899
Effective search space used:   136899
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: 50 (23.9 bits)

Align candidate CCNA_03750 CCNA_03750 (threonine dehydratase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.2814689.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-129  417.4   0.0   3.2e-129  417.2   0.0    1.0  1  FitnessBrowser__Caulo:CCNA_03750  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_03750  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   0.0  3.2e-129  3.2e-129       1     377 [.      22     396 ..      22     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 3.2e-129
                         TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgikakiv 77 
                                       tp  +s+tls+itgaev++k enlq t ++k rGalnk+  lse ek+rGv+aasaGnhaqG a+   + g++ +iv
  FitnessBrowser__Caulo:CCNA_03750  22 TPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKLMLLSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIV 98 
                                       8999************************************************************************* PP

                         TIGR01127  78 mPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledlpdvdtviv 154
                                       mP+ +p  kv+ t+ +Ga v+++G+++D+a ++a++l +e+g++fvh+fdD  ++aGqGt++le+led pd++++ v
  FitnessBrowser__Caulo:CCNA_03750  99 MPKTTPFVKVQHTRDFGATVVIEGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPV 175
                                       ***************************************************************************** PP

                         TIGR01127 155 PvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdltfeivkelvDev 231
                                       P+GGGGLisGva+a+k l+p++++iG e    ps+++ ++   + a+   +tia+G+avk++g+lt+ +v+ l D+v
  FitnessBrowser__Caulo:CCNA_03750 176 PIGGGGLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRG--VAAHCGGQTIAEGVAVKQVGELTYGVVRPLLDDV 250
                                       ***************************98888888887654..6788899*************************** PP

                         TIGR01127 232 vavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnllekiiekgLvksgrkvki 308
                                       +  +e  + +a+ l  + +k++aegaGa+++aa+l+      gkk +++++GGnid++ll  +++++Lv+  r++ +
  FitnessBrowser__Caulo:CCNA_03750 251 LLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLILCGGNIDTRLLASVLTRELVRAQRLASL 327
                                       ************************************9888************************************* PP

                         TIGR01127 309 etvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehleellktlrdkgye 377
                                       + +  D+PG L +++ vi   +ani++++h+rl+ +++   a+  +++e+++ +h +e+++ lr+ gy 
  FitnessBrowser__Caulo:CCNA_03750 328 RIIGDDRPGLLSTVASVIGAMGANIIEVNHNRLALDVPAKGAEFDITIETRDAQHTQEVMEALRESGYP 396
                                       *******************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (400 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 23.47
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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