Alignments for a candidate for thrC in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Crocosphaera subtropica ATCC 51142

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_009544859.1 CCE_RS11565 threonine synthase

Query= curated2:Q58860
         (405 letters)



>NCBI__GCF_000017845.1:WP_009544859.1
          Length = 435

 Score =  275 bits (702), Expect = 2e-78
 Identities = 156/380 (41%), Positives = 223/380 (58%), Gaps = 6/380 (1%)

Query: 27  LEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKDESKIVSLCEGGTPLYRCNNLEKE 86
           LE+ YDY+ I+ +VS E +      +WRY  +LPV  E+ I  +  G TPL +   L + 
Sbjct: 44  LEVAYDYDAIRAQVSRETIEAGPNSIWRYKAFLPVNSENPI-DVGTGMTPLVKSTRLARR 102

Query: 87  LGIKELYVKNEGAN-PTGSFKDRGMTVGVTRANELGVEVVGCASTGNTSASLAAYSARSG 145
           LG+  LY+KN+  N PT SFKDR ++V +TRA ELG   V CASTGN + S AA +A +G
Sbjct: 103 LGLNNLYIKNDAVNMPTLSFKDRVVSVALTRAKELGFTTVSCASTGNLANSTAAIAAHAG 162

Query: 146 KKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALDMVKQLAKEKLIYLLN-SINPF 204
             C V +P    A GK+   + Y   V+ VKGN+D    +  ++        +N ++ P+
Sbjct: 163 LDCCVFIPSDLEA-GKVLGTLIYNPTVMAVKGNYDQVNRLCCEVGNTYGWGFVNINLRPY 221

Query: 205 RLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWKGFKEFEITGII-DELPKMTGI 263
             EG KT+ FE+ +QL W++PD V+ P+ +    + I+KGF+EF  TG++ D+  + +G 
Sbjct: 222 YSEGSKTLGFEVAEQLGWKLPDHVVAPLASGSLYTKIYKGFQEFIKTGLVEDKAVRFSGA 281

Query: 264 QADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGNPVNAPKALDAIYSSGGYAEAVTDE 323
           QA+G  PI  AF K  +D +    P TIA +I IGNP +   ALD    + G  E+VTD 
Sbjct: 282 QAEGCSPIASAF-KEGRDFVTPVKPNTIAKSIAIGNPADGYYALDIARKTNGNIESVTDA 340

Query: 324 EIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDRDERIVCITTGHGLKDPDAAIR 383
           EIVE  KLLA  EGIF E A  +++A LKKL+E G ID DE  V   TG+GLK  +A   
Sbjct: 341 EIVEGIKLLAETEGIFTETAGGTTVAVLKKLVEAGKIDPDETTVVYITGNGLKTQEAVQE 400

Query: 384 ASEEPIKIECDMNVLKRILK 403
              +P+ IE  ++  +R L+
Sbjct: 401 YIGQPLTIEPKLDSFERALE 420


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: 493
Number of extensions: 31
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: 435
Length adjustment: 32
Effective length of query: 373
Effective length of database: 403
Effective search space:   150319
Effective search space used:   150319
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_009544859.1 CCE_RS11565 (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.2633.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-107  346.0   0.0   1.4e-107  345.8   0.0    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009544859.1  CCE_RS11565 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009544859.1  CCE_RS11565 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.8   0.0  1.4e-107  1.4e-107       1     340 []      69     396 ..      69     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 345.8 bits;  conditional E-value: 1.4e-107
                                 TIGR00260   1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhg.PtlaFKDrglqfvavlltka 68 
                                               ++ry+++l+v+ ++++d+ +g+t+l++s +la+++g++nly+k+++++ Ptl+FKDr+   v+v+lt+a
  lcl|NCBI__GCF_000017845.1:WP_009544859.1  69 IWRYKAFLPVNSENPIDVGTGMTPLVKSTRLARRLGLNNLYIKNDAVNmPTLSFKDRV---VSVALTRA 134
                                               8*********************************************************...******** PP

                                 TIGR00260  69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137
                                               +elg +tv cA++G++++++a a+a++a+++++v++P++ ++  ++k++ +l++n +v+a+kG++D+++
  lcl|NCBI__GCF_000017845.1:WP_009544859.1 135 KELGFTTVSCASTGNLANSTA-AIAAHAGLDCCVFIPSD-LE--AGKVLGTLIYNPTVMAVKGNYDQVN 199
                                               *********************.*****************.88..9************************ PP

                                 TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205
                                               +l++e+  + + ++++++N++ p++ e++kt+ fe++eqlg++ pd+vv p++ +++ ++i+kGf+e+ 
  lcl|NCBI__GCF_000017845.1:WP_009544859.1 200 RLCCEVG-NTYGWGFVNINLR-PYYSEGSKTLGFEVAEQLGWKLPDHVVAPLAsGSLYTKIYKGFQEFI 266
                                               ******9.899********88.*******************************666779********** PP

                                 TIGR00260 206 elg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270
                                               ++g    + +++++++aeg+++i+ +f++++d+++  +++T++++++ignp++  +al++ar+++gn+e
  lcl|NCBI__GCF_000017845.1:WP_009544859.1 267 KTGlvedKAVRFSGAQAEGCSPIASAFKEGRDFVTPVKPNTIAKSIAIGNPADGYYALDIARKTNGNIE 335
                                               ****99999************************************************************ PP

                                 TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339
                                               ++    +d+ei+e ik+lae+eg+++e++++++va+lkklve+g   ++dp+  e++v+++tgn+lk++
  lcl|NCBI__GCF_000017845.1:WP_009544859.1 336 SV----TDAEIVEGIKLLAETEGIFTETAGGTTVAVLKKLVEAG---KIDPD--ETTVVYITGNGLKTQ 395
                                               **....**************************************...*****..*************98 PP

                                 TIGR00260 340 e 340
                                               e
  lcl|NCBI__GCF_000017845.1:WP_009544859.1 396 E 396
                                               7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (435 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: 12.06
//
[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