Alignments for a candidate for thrC in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Haloglycomyces albus DSM 45210

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_025272738.1 HALAL_RS0103875 threonine synthase

Query= curated2:Q58860
         (405 letters)



>NCBI__GCF_000527155.1:WP_025272738.1
          Length = 421

 Score =  246 bits (628), Expect = 9e-70
 Identities = 144/382 (37%), Positives = 219/382 (57%), Gaps = 9/382 (2%)

Query: 5   CIKCGKTYDVDEIIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKD- 63
           C  C KTYD+       +C G LE+ YD   +  +V+ E++      +WRY   LPV + 
Sbjct: 18  CRNCEKTYDLIAQHACWQCFGPLEVEYDSTALA-RVTREQIEAGPHNIWRYAGLLPVGNI 76

Query: 64  ESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVE 123
            S  VSL  G TPL   +NL +ELG+++L+VK++ ANPT SFKDR ++V +T A  LG +
Sbjct: 77  ASDRVSLNPGMTPLIEADNLARELGMRKLWVKDDSANPTHSFKDRVVSVALTAAGYLGFD 136

Query: 124 VVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDAL 183
              CASTGN + S+AA+ AR+G++ IV +P   +  GK+     YG  ++ V+G++DD  
Sbjct: 137 RFACASTGNLANSVAAHGARAGRESIVFIPH-DLERGKVITTAVYGGSLVAVRGSYDDVN 195

Query: 184 DMVKQLAK----EKLIYLLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNIS 239
            +   L +    E   ++  +I PF  EG KT+ +E+ +QL W++P++V++P  +   ++
Sbjct: 196 RLCSMLCETDEFENTAFVNVNIRPFYAEGSKTLGYEVAEQLGWRLPEQVVIPAASGELLT 255

Query: 240 AIWKGFKEFEITGIIDE-LPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIG 298
            + K F +    G+ D    ++ G Q+ G  PI +AF      I P K P  IA ++ IG
Sbjct: 256 KVHKAFDDCVDIGLTDSGKVRVFGAQSAGCSPISDAFNADTDVIDPVK-PTGIAKSLNIG 314

Query: 299 NPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEG 358
           +P   P A+++  S+GG  + V D+EI E  +LLA   GIF E A   S+A L+KLL +G
Sbjct: 315 DPAAGPYAIESARSTGGAFDKVDDDEIREGIRLLAATTGIFAETAGGVSVAVLRKLLRDG 374

Query: 359 IIDRDERIVCITTGHGLKDPDA 380
            +D D   V   TG GLK  DA
Sbjct: 375 KLDPDAETVVYNTGEGLKTLDA 396


Lambda     K      H
   0.317    0.137    0.395 

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: 482
Number of extensions: 27
Number of successful extensions: 7
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: 421
Length adjustment: 31
Effective length of query: 374
Effective length of database: 390
Effective search space:   145860
Effective search space used:   145860
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_025272738.1 HALAL_RS0103875 (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.6095.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.1e-77  246.5   0.0    2.4e-77  246.3   0.0    1.0  1  lcl|NCBI__GCF_000527155.1:WP_025272738.1  HALAL_RS0103875 threonine syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000527155.1:WP_025272738.1  HALAL_RS0103875 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.3   0.0   2.4e-77   2.4e-77       1     339 [.      64     394 ..      64     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 246.3 bits;  conditional E-value: 2.4e-77
                                 TIGR00260   1 vvryreilevt..ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltk 67 
                                               ++ry+ +l+v    +d v+l+ g+t+l+++++la+e+g+++l+vk+++++Pt +FKDr+   v+v+lt+
  lcl|NCBI__GCF_000527155.1:WP_025272738.1  64 IWRYAGLLPVGniASDRVSLNPGMTPLIEADNLARELGMRKLWVKDDSANPTHSFKDRV---VSVALTA 129
                                               8*********9899*********************************************...******* PP

                                 TIGR00260  68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136
                                               a  lg +  +cA++G++++++a a+ ++a+ + +v++P++ ++   +k++t+ +++  ++a++G +Dd+
  lcl|NCBI__GCF_000527155.1:WP_025272738.1 130 AGYLGFDRFACASTGNLANSVA-AHGARAGRESIVFIPHD-LE--RGKVITTAVYGGSLVAVRGSYDDV 194
                                               **********************.*****************.99..************************ PP

                                 TIGR00260 137 qdlvkeifedke..klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsg.nfgailkGfl 202
                                               ++l+  ++e +e  ++ +++vN i p++ e++kt+ +e++eqlg++ p++vv+p +sg ++++++k+f 
  lcl|NCBI__GCF_000527155.1:WP_025272738.1 195 NRLCSMLCETDEfeNTAFVNVN-IRPFYAEGSKTLGYEVAEQLGWRLPEQVVIPAASGeLLTKVHKAFD 262
                                               *********665579*******.67*******************************773689******* PP

                                 TIGR00260 203 ekkelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslg 267
                                                    g      ++  ++++ g+++i ++f  + d+    ++  ++++++ig p+  ++a e ar+++g
  lcl|NCBI__GCF_000527155.1:WP_025272738.1 263 DCVDIGltdsGKVRVFGAQSAGCSPISDAFNADTDVIDPVKPTGIAKSLNIGDPAAGPYAIESARSTGG 331
                                               ******9888789******************************************************** PP

                                 TIGR00260 268 nledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnkl 336
                                                ++++     d+ei e i++la++ g+++e++++v+va+l+kl+ +g   ++dp+  +e+v++ tg++l
  lcl|NCBI__GCF_000527155.1:WP_025272738.1 332 AFDKV----DDDEIREGIRLLAATTGIFAETAGGVSVAVLRKLLRDG---KLDPD--AETVVYNTGEGL 391
                                               *****....**************************************...*****..************ PP

                                 TIGR00260 337 kdp 339
                                               k+ 
  lcl|NCBI__GCF_000527155.1:WP_025272738.1 392 KTL 394
                                               985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (421 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: 00:00:00.01
# Mc/sec: 8.81
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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:

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
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