GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Halococcus hamelinensis 100A6

Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_007691417.1 C447_RS04700 threonine synthase

Query= CharProtDB::CH_107419
         (405 letters)



>NCBI__GCF_000336675.1:WP_007691417.1
          Length = 417

 Score =  402 bits (1033), Expect = e-116
 Identities = 222/399 (55%), Positives = 271/399 (67%), Gaps = 13/399 (3%)

Query: 4   LKCIECGAEYSR-DEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLPVE 62
           L CIECG   +  DE  Y C  CDGLL+  Y+      D          VW+YA  LP E
Sbjct: 20  LACIECGRTLAPFDEPTYRCPDCDGLLEARYEEYPTFEDFSGR-----GVWRYAAALPFE 74

Query: 63  REPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGMNT 122
              V++ EG TPL++  RL   +G++ L VKHEGMNPTGSFKDRGMTVGV  A ELG++ 
Sbjct: 75  -SGVSLPEGDTPLHEVPRLEADVGVRSLRVKHEGMNPTGSFKDRGMTVGVRVAQELGVDR 133

Query: 123 VACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDALA 182
           +ACASTGNTSAALA YG +AG+  +VLLPAGKVA GKVAQA +HGA++L + GNFD  L 
Sbjct: 134 LACASTGNTSAALAAYGGRAGVETLVLLPAGKVAAGKVAQAALHGARILEVDGNFDACLD 193

Query: 183 LVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQL---DFKVPDRIVLPVGNAGNITAI 239
           +V  L +  + YLLNS+NP+RLEGQKTIGFEI +       + PDRIVLPVGNAGN  A+
Sbjct: 194 VVAELANMGEAYLLNSLNPFRLEGQKTIGFEILESFLAEYDRYPDRIVLPVGNAGNTAAL 253

Query: 240 YKGFREFKILGITD--SLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGN 297
           YK FRE    G  D   +P +TG+QAEG+ P+V+AI+ G       E+ ET ATAIRIGN
Sbjct: 254 YKAFRELVEAGALDEAEVPMLTGVQAEGAAPMVEAIEEGLDDTRRWEDVETRATAIRIGN 313

Query: 298 PVNATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGV 357
           PVNA KAL  IR +GGTA +V DE I+ AQ+ LA  EG+GVEPASAAS+AGLRKL + G 
Sbjct: 314 PVNARKALPGIRGTGGTAVAVADEAIVDAQRTLAE-EGVGVEPASAASIAGLRKLRESGT 372

Query: 358 IGRDETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAI 396
           +  DE VVC+TTGHLLKDP        +P  V  + +AI
Sbjct: 373 VDDDEDVVCLTTGHLLKDPDAAAAAGRDPEPVPNDTEAI 411


Lambda     K      H
   0.317    0.135    0.389 

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: 551
Number of extensions: 34
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: 405
Length of database: 417
Length adjustment: 31
Effective length of query: 374
Effective length of database: 386
Effective search space:   144364
Effective search space used:   144364
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_007691417.1 C447_RS04700 (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.1265849.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      8e-92  293.9   0.0    9.1e-92  293.7   0.0    1.0  1  NCBI__GCF_000336675.1:WP_007691417.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000336675.1:WP_007691417.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.7   0.0   9.1e-92   9.1e-92       1     340 []      64     392 ..      64     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 293.7 bits;  conditional E-value: 9.1e-92
                             TIGR00260   1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 
                                           v+ry+++l+      v+l eg t+l ++p+l++ vg++ l vk+++++Pt++FKDrg   ++v++  a+elg+
  NCBI__GCF_000336675.1:WP_007691417.1  64 VWRYAAALPFE--SGVSLPEGDTPLHEVPRLEADVGVRSLRVKHEGMNPTGSFKDRG---MTVGVRVAQELGV 131
                                           8********97..99******************************************...************* PP

                             TIGR00260  74 etvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifed 146
                                           + ++cA++G+t+aa+a a+ g+a+v+ +vL+P+gk++  ++k+++a  ++a++l+++G+FD+++d+v+e++++
  NCBI__GCF_000336675.1:WP_007691417.1 132 DRLACASTGNTSAALA-AYGGRAGVETLVLLPAGKVA--AGKVAQAALHGARILEVDGNFDACLDVVAELANM 201
                                           ****************.********************..********************************** PP

                             TIGR00260 147 keklklnsvNsinparieaqktyafeiveqlgk...espdkvvvpvp.sgnfgailkGflekkelg......l 209
                                            e+++lns N   p+r+e+qkt+ fei+e       + pd++v+pv+ +gn  a++k+f e+ e+g      +
  NCBI__GCF_000336675.1:WP_007691417.1 202 GEAYLLNSLN---PFRLEGQKTIGFEILESFLAeydRYPDRIVLPVGnAGNTAALYKAFRELVEAGaldeaeV 271
                                           *********9...***************9987656689********************************888 PP

                             TIGR00260 210 pieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeei 281
                                           p + ++++aegaa++v++  ++  d    ed+eT +tA++ignp+n+ +al ++r ++g + ++     de+i
  NCBI__GCF_000336675.1:WP_007691417.1 272 P-MLTGVQAEGAAPMVEAIEEGLdDTRRWEDVETRATAIRIGNPVNARKALPGIRGTGGTAVAV----ADEAI 339
                                           8.899**************8888666677888*****************************999....99999 PP

                             TIGR00260 282 leaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340
                                           ++a++ la eeg+ +ep++a+++a+l+kl e+g   t+d +  e+vv+  tg+ lkdp+
  NCBI__GCF_000336675.1:WP_007691417.1 340 VDAQRTLA-EEGVGVEPASAASIAGLRKLRESG---TVDDD--EDVVCLTTGHLLKDPD 392
                                           99987765.78**********************...*****..**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (417 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: 25.42
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

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:

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:

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:

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