Aligments for a candidate for thrC in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for thrC in Caulobacter crescentus NA1000

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate CCNA_03510 CCNA_03510 threonine synthase

Query= curated2:P29363
         (469 letters)



>FitnessBrowser__Caulo:CCNA_03510
          Length = 465

 Score =  422 bits (1084), Expect = e-122
 Identities = 221/459 (48%), Positives = 293/459 (63%), Gaps = 1/459 (0%)

Query: 1   MRYISTRGQAPALNFEDVLLAGLASDGGLYVPENLPRFTLEEIASWVGLPYHELAFRVMR 60
           MRY+STRGQ+  + F D +LAGLA DGGLYVP   P FT ++IA++ G PY E+A  V+ 
Sbjct: 1   MRYVSTRGQSAPIGFLDAVLAGLAPDGGLYVPAEWPSFTAKQIAAFAGKPYAEVAAAVVG 60

Query: 61  PFVAGSIADADFKKILEETYGVFAHDAVAPLRQLNGNEWVLELFHGPTLAFKDFALQLLG 120
            FV   I   D  ++ EE Y  FAH AV P++QL  N ++LELFHGPTLAFKD A+QLLG
Sbjct: 61  KFVGDDIPADDLLQMCEEAYATFAHTAVTPVKQLTANRYLLELFHGPTLAFKDVAMQLLG 120

Query: 121 RLLDHVLAKRGERVVIMGATSGDTGSAAIEGCRRCDNVDIFIMHPHNRVSEVQRRQMTTI 180
           RL D+VL ++  ++ I+ ATSGDTG AA+E  R   N  I  + P  R+SEVQRR MTT 
Sbjct: 121 RLYDYVLERQSRKMTIICATSGDTGGAAVEAFRGRKNARIVALFPEGRISEVQRRFMTTA 180

Query: 181 LGDNIHNIAIEGNFDDCQEMVKASFADQGFLKGTRLVAVNSINWARIMAQIVYYFHAALQ 240
              N+  +++ G+FDDCQ +VK +F D  F     L  VNSINWARI AQ VYYF AA+ 
Sbjct: 181 TDANVACVSVLGSFDDCQAIVKQAFQDDQFRHAVDLSGVNSINWARIAAQSVYYFTAAVA 240

Query: 241 LGAPHRSVAFSVPTGNFGDIFAGYLARNMGLPVSQLIVATNRNDILHRFMSGNRYDKDTL 300
           LGAP R VAF VPTGNFGD +A ++A+ +GLP+  +  ATN NDIL R     RY +  +
Sbjct: 241 LGAPAREVAFVVPTGNFGDAYAAFVAKTLGLPIHSVTAATNSNDILARAFEDGRYSRGAV 300

Query: 301 HPSLSPSMDIMVSSNFERLLFDLHGRNGKAVAELLDAFKASGKLSVEDQRWTEARKLFDS 360
             + SP+MDI V+SNFERL F+   R+G        AF  +G L +        R+LF  
Sbjct: 301 AATQSPAMDIQVASNFERLYFEAVRRDGVETGRAFRAFADTGLLDIPPAAHAWMRELFRG 360

Query: 361 LAVSDEQTCETIAEVYRSSGELLDPHTAIGVRAARECRRSLSVPMVTLGTAHPVKFPEAV 420
            +VS+  T +T+      +GE++DPHTA+G+ AA+  R   ++P+V L TAHP KFPEAV
Sbjct: 361 ASVSEADTAKTMLSTLNETGEVVDPHTAVGLAAAQGVRIDPAIPVVVLSTAHPAKFPEAV 420

Query: 421 EKAGIGQAPALPAHLADLFEREERCTVLPNELAKVQAFV 459
           + A  G  P+ P    DL ++ E+   LP + + V+AFV
Sbjct: 421 Q-AATGLLPSTPRATPDLSKKPEKFERLPADGSSVKAFV 458


Lambda     K      H
   0.322    0.137    0.407 

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: 541
Number of extensions: 22
Number of successful extensions: 2
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: 469
Length of database: 465
Length adjustment: 33
Effective length of query: 436
Effective length of database: 432
Effective search space:   188352
Effective search space used:   188352
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_03510 CCNA_03510 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.5825.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    7.9e-84  267.6   0.1    1.1e-83  267.2   0.1    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03510  CCNA_03510 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03510  CCNA_03510 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.2   0.1   1.1e-83   1.1e-83      12     333 ..      69     425 ..      63     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 267.2 bits;  conditional E-value: 1.1e-83
                             TIGR00260  12 ekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 
                                             dl++++e  +++f+  +++  ++++a n y++elfhgPtlaFKD+++q ++ l  ++le++    t++cAt
  lcl|FitnessBrowser__Caulo:CCNA_03510  69 ADDLLQMCEEAYATFAHTAVTpvKQLTA-NRYLLELFHGPTLAFKDVAMQLLGRLYDYVLERQSRkmTIICAT 140
                                           4689999*********999998899999.99*****************************9998888****** PP

                             TIGR00260  81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...k 149
                                           sGdtg aa+ea++g++n ++v L P+g+is v    ++ta + n+  +++ G FDd+q++vk++f+d++   +
  lcl|FitnessBrowser__Caulo:CCNA_03510 141 SGDTGGAAVEAFRGRKNARIVALFPEGRISEVqRRFMTTATDANVACVSVLGSFDDCQAIVKQAFQDDQfrhA 213
                                           ********************************77779999**************************8877999 PP

                             TIGR00260 150 lklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaa 222
                                           + l+ vNsin+ari+aq +y+f ++ +lg     +v+++vp gnfg+++++f++k +lglpi+   +a++++ 
  lcl|FitnessBrowser__Caulo:CCNA_03510 214 VDLSGVNSINWARIAAQSVYYFTAAVALG-APAREVAFVVPTGNFGDAYAAFVAK-TLGLPIHSVTAATNSN- 283
                                           9****************************.56668****************7765.566******9999998. PP

                             TIGR00260 223 divrrflksgdlepkedkeTlstAmdignpsnverale.larrslgn.ledlke................... 274
                                           di+ r  ++g  +  +  +T s+Amdi   sn+er+ + ++rr + + + + ++                   
  lcl|FitnessBrowser__Caulo:CCNA_03510 284 DILARAFEDGRYSRGAVAATQSPAMDIQVASNFERLYFeAVRRDGVEtGRAFRAfadtglldippaahawmre 356
                                           **99999*9988888888******************99888887655145555599***************** PP

                             TIGR00260 275 .....svsdeeileaikklaeeegyllephtavavaalkklvekg....vs.atadpaKFeevvealtg 333
                                                svs++++ +++   ++e g +++phtav++aa +    +     v  +ta+paKF+e+v+a tg
  lcl|FitnessBrowser__Caulo:CCNA_03510 357 lfrgaSVSEADTAKTMLSTLNETGEVVDPHTAVGLAAAQGVRIDPaipvVVlSTAHPAKFPEAVQAATG 425
                                           ************************************9987644444775226*************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (465 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: 14.96
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or view the source code, or see 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