Alignments for a candidate for tdcB in Planktomarina temperata RCA23

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Planktomarina temperata RCA23

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_044051092.1 RCA23_RS15620 threonine ammonia-lyase IlvA

Query= BRENDA::Q04513
         (436 letters)



>NCBI__GCF_000738435.1:WP_044051092.1
          Length = 411

 Score =  303 bits (777), Expect = 5e-87
 Identities = 173/396 (43%), Positives = 238/396 (60%), Gaps = 9/396 (2%)

Query: 29  AQARISSVIAPTPLQYCPRLSEETGAEIYLKREDLQDVRSYKIRGALNSGAQLTQEQRDA 88
           A  R+  +   TPLQ    LS    A+I+LKREDL  VRSYK+RGA N+  +  Q  +D 
Sbjct: 11  ATERMRQLFPATPLQRNDHLSNVYDADIWLKREDLSPVRSYKLRGAFNAMGK--QADKDV 68

Query: 89  GIVAASAGNHAQGVAYVCKSLGVQGRIYVPVQTPKQKRDRIMVHGGEFVSLVVTGNNFDE 148
             V ASAGNHAQGVAYVC+ L  +G I++PV TP+QK  +  + GG +V + + G+ FD+
Sbjct: 69  -FVCASAGNHAQGVAYVCRHLQKKGVIFMPVTTPEQKIRKTRLFGGAWVQVQLVGDYFDD 127

Query: 149 ASAAAHEDAERTGATLIEPFDARNTVIGQGTVAAEILSQLTSMGKSADHVMVPVGGGGLL 208
              A+       G   + PFD  + + GQ TV  E+L QL   G+S D  +VPVGGGGL 
Sbjct: 128 TLRASQAYCAEVGGHFLSPFDDPDVIEGQATVTYEMLEQL---GRSPDVFVVPVGGGGLS 184

Query: 209 AGVVSYMADMAPRTAIVGIEPAGAASMQAALHNGGPITLETVDPFVDGAAVKRVGDLNYT 268
           +     +++ AP T I  +EP+G  S+ AA+  G PI LE VD FVDGAAV ++G +N  
Sbjct: 185 SSARRLLSERAPETEIFYVEPSGGKSLAAAVQAGAPIALEQVDTFVDGAAVAKMG-VNTF 243

Query: 269 IVEKNQGRVHMMSATEGAVCTEMLDLYQNEGIIAEPAGALSIAGLKEM-SFAPGSVVVCI 327
              K     H++   E  +CT +LD+   EGI+ EPAGAL++  LK++     G  VVC+
Sbjct: 244 AALKGIDADHVLDIPEDRICTTILDMLNTEGIVLEPAGALALDALKDLKDKIKGKTVVCV 303

Query: 328 ISGGNNDVLRYAEIAERSLVHRGLKHYFLVNFPQKPGQLRHFLEDILGPDDDITLFEYLK 387
            SGGN D  R  E+ ER+  + G+K YF++  PQ+PG L+ FL  +LGPDDDI  FEYLK
Sbjct: 304 SSGGNFDFERLPEVKERAQRYAGVKKYFILRLPQRPGALKDFL-GLLGPDDDIARFEYLK 362

Query: 388 RNNRETGTALVGIHLSEASGLDSLLERMEESAIDSR 423
           ++ R  GT L+GI  S+      L ER+E + +  R
Sbjct: 363 KSARNFGTVLLGIETSKPENFALLSERLEAAGMSIR 398


Lambda     K      H
   0.316    0.133    0.373 

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: 419
Number of extensions: 22
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: 436
Length of database: 411
Length adjustment: 32
Effective length of query: 404
Effective length of database: 379
Effective search space:   153116
Effective search space used:   153116
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_044051092.1 RCA23_RS15620 (threonine ammonia-lyase IlvA)
to HMM TIGR02079 (ilvA: threonine dehydratase (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/TIGR02079.hmm
# target sequence database:        /tmp/gapView.426375.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02079  [M=410]
Accession:   TIGR02079
Description: THD1: threonine dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-161  523.9   0.0   1.5e-161  523.7   0.0    1.0  1  NCBI__GCF_000738435.1:WP_044051092.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000738435.1:WP_044051092.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.7   0.0  1.5e-161  1.5e-161       4     410 .]       9     411 .]       6     411 .] 0.98

  Alignments for each domain:
  == domain 1  score: 523.7 bits;  conditional E-value: 1.5e-161
                             TIGR02079   4 ekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvcasaGnha 76 
                                            +a++r+++++  tPlq+n++ls+ y+a+i+lkredl+ vrsyklrGa+n++ + +d   ++++vcasaGnha
  NCBI__GCF_000738435.1:WP_044051092.1   9 AEATERMRQLFPATPLQRNDHLSNVYDADIWLKREDLSPVRSYKLRGAFNAMGKQAD---KDVFVCASAGNHA 78 
                                           6899**********************************************9976555...569********** PP

                             TIGR02079  77 qGvayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfddkd 149
                                           qGvay cr+l+ kg++fmPvttP+qk+ k++lfGg +++v lvGd fd++  a++  +++ g +++ Pfdd+d
  NCBI__GCF_000738435.1:WP_044051092.1  79 QGVAYVCRHLQKKGVIFMPVTTPEQKIRKTRLFGGAWVQVQLVGDYFDDTLRASQAYCAEVGGHFLSPFDDPD 151
                                           ************************************************************************* PP

                             TIGR02079 150 iieGqgtvaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkagevvtl 222
                                           +ieGq+tv+ e+leql  + +d+ +vpvGGGGl+s    +l e++++t+i +veP+G  sl a+++ag ++ l
  NCBI__GCF_000738435.1:WP_044051092.1 152 VIEGQATVTYEMLEQLGRS-PDVFVVPVGGGGLSSSARRLLSERAPETEIFYVEPSGGKSLAAAVQAGAPIAL 223
                                           *****************97.***************************************************** PP

                             TIGR02079 223 dkidkfvdGaavkrvGdlnfkalkkvvd.evtlveegavcstildlynkegivaePaGalsiaaleelseeik 294
                                           +++d fvdGaav+++G  +f+alk + + +v  ++e+++c+tild++n+egiv+ePaGal++ al+ l+++ik
  NCBI__GCF_000738435.1:WP_044051092.1 224 EQVDTFVDGAAVAKMGVNTFAALKGIDAdHVLDIPEDRICTTILDMLNTEGIVLEPAGALALDALKDLKDKIK 296
                                           *************************987699****************************************** PP

                             TIGR02079 295 gktvvcvvsGgnndierleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksnret 367
                                           gktvvcv sGgn+d+erl+e+ker+ +y G+k+yf++++pqr+Gal++fl  +lGP+ddi++fey+kks+r++
  NCBI__GCF_000738435.1:WP_044051092.1 297 GKTVVCVSSGGNFDFERLPEVKERAQRYAGVKKYFILRLPQRPGALKDFLG-LLGPDDDIARFEYLKKSARNF 368
                                           **************************************************9.********************* PP

                             TIGR02079 368 GevliGielsdkedfeGllerlkaadieyeainenetlyellv 410
                                           G vl+Gie+s+ e+f+ l erl+aa++++++i+ +e + +l++
  NCBI__GCF_000738435.1:WP_044051092.1 369 GTVLLGIETSKPENFALLSERLEAAGMSIRDITGDEAMVDLII 411
                                           ************************************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (410 nodes)
Target sequences:                          1  (411 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 15.49
//
[ok]

This GapMind analysis is from Sep 24 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 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