Alignments for a candidate for thrC in Nitratifractor salsuginis DSM 16511

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Nitratifractor salsuginis DSM 16511

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_013553364.1 NITSA_RS02035 threonine synthase

Query= curated2:O24924
         (486 letters)



>NCBI__GCF_000186245.1:WP_013553364.1
          Length = 488

 Score =  419 bits (1078), Expect = e-122
 Identities = 234/491 (47%), Positives = 304/491 (61%), Gaps = 12/491 (2%)

Query: 1   MPFVPTRSLKEKK---IDFIEAILNPNAPKGGLYTLERFETLQ---WQDCLNLSYNDLVE 54
           M F+ TR    K    + F EAILNP A  GGLY  E    +      + L   Y  L  
Sbjct: 1   MQFIETRGNDGKNPAAVPFSEAILNPRASYGGLYVPESLPDMSIGFLSEYLQSDYKTLAF 60

Query: 55  CVFERLGLEIPKNLLASALKRYENFDNPKNPAPIFALNERLFVQELYHGPSLAFKDMALQ 114
            + +   ++I   LL  AL+RY+ FD+P NP P+  + E L+V ELYHGP+ AFKDMALQ
Sbjct: 61  ALLKAFEIDIDDELLHKALERYDRFDDPNNPVPVVGIEEDLYVSELYHGPTRAFKDMALQ 120

Query: 115 PLASLFSNLAVGKNEKYLMLVSTSGDTGPATLESLAGMPNVFVVCLYPKDGTSLVQKLQM 174
           P   + S LA  +NE+YL++ +TSGDTGPATLE+     N+ V CLYP+ GTS VQ+LQM
Sbjct: 121 PFGVILSTLAKRRNERYLIMAATSGDTGPATLETFKNRENIKVTCLYPEGGTSDVQRLQM 180

Query: 175 VTQSASNLKVFGISGDFDDAQNALKNLLKDDDFNEALKACQLKLSVANSVNFGRIAFQIV 234
           VT+ A NLKV G+ G+FDD Q+ALK LL  + F E L+   LKLS ANSVNFGRI FQI+
Sbjct: 181 VTEDAPNLKVIGVKGNFDDTQHALKELLSSETFREELRKRDLKLSAANSVNFGRIIFQII 240

Query: 235 YHIWGFLELYKKGAINSKEKITLAIPSGNFGNALGAFYAKKMGLNIDKIKVVTNSNDVLR 294
           YHI  +LEL ++  I   E+I L +PSGNFGNALGA+YAKK GL + KI + +N+N++L 
Sbjct: 241 YHIHSYLELVRQNVITLGEEIYLVVPSGNFGNALGAYYAKKAGLPVRKILIASNANNILT 300

Query: 295 EFIETGRYDLTHRSLKQTYSPAMDILKSSNVERALFSLFGFERTLELMQALEEEKFYALK 354
           ++I  G YDL  R L QT SPAMDIL SSNVER L+  FG ERT ELM+AL +E  Y+L 
Sbjct: 301 DWIRKGEYDLRGRCLIQTESPAMDILISSNVERVLYDKFGPERTRELMEALSKEGHYSLT 360

Query: 355 PKELALLQEHFSCASCSDEACLKTIQEVYAEHQYLIDPHTATALNASLKTHEK---TLVS 411
           P+EL  LQE F     SDE   K I   YAE  YL+DPHTAT L A  +   +   T++ 
Sbjct: 361 PEELKSLQEDFDATFSSDEEGEKIIAR-YAERGYLMDPHTATCLKAYRELRREPLATVIY 419

Query: 412 ATASYEKFPRITLLALNEQKKNDNDKAALETLKNSYNTPDSQRLDDLFERGIKHQEVLKL 471
           +TA + KF R    A+      + DK AL+ +         + + +LF + I H  V++ 
Sbjct: 420 STAEWTKFSRTVARAIGIAA--ETDKEALDAVSRKLGVLIPKVISELFNKPIVHTTVVEK 477

Query: 472 NEIKSSILLWL 482
            EI   +L +L
Sbjct: 478 EEIMQEMLSFL 488


Lambda     K      H
   0.318    0.134    0.381 

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: 575
Number of extensions: 22
Number of successful extensions: 4
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: 486
Length of database: 488
Length adjustment: 34
Effective length of query: 452
Effective length of database: 454
Effective search space:   205208
Effective search space used:   205208
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_013553364.1 NITSA_RS02035 (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.1809196.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-85  273.1   0.0    2.3e-85  272.7   0.0    1.1  1  NCBI__GCF_000186245.1:WP_013553364.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000186245.1:WP_013553364.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.7   0.0   2.3e-85   2.3e-85       8     333 ..      66     436 ..      61     444 .. 0.92

  Alignments for each domain:
  == domain 1  score: 272.7 bits;  conditional E-value: 2.3e-85
                             TIGR00260   8 levt.ekdlvdlaegstelfrspklaeevga..enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..t 75 
                                            e+  + +l+  a  ++  f+ p+++ +v +  e+lyv el+hgPt aFKD++lq+ +v+l+ ++++ ne  +
  NCBI__GCF_000186245.1:WP_013553364.1  66 FEIDiDDELLHKALERYDRFDDPNNPVPVVGieEDLYVSELYHGPTRAFKDMALQPFGVILSTLAKRRNEryL 138
                                           555567778888889999*****99987766699************************************99* PP

                             TIGR00260  76 vlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedk 147
                                           ++ AtsGdtg+a++e ++ ++n+kv +LyP+g++s v   ++vt  a n+kv+++kG+FDd q+++ke+++ +
  NCBI__GCF_000186245.1:WP_013553364.1 139 IMAATSGDTGPATLETFKNRENIKVTCLYPEGGTSDVqRLQMVTEDAPNLKVIGVKGNFDDTQHALKELLSSE 211
                                           *************************************99*******************************955 PP

                             TIGR00260 148 e........klklnsvNsinparieaqk.tyafeiveqlgk...espdkvvvpvpsgnfgailkGflekkelg 208
                                                     lkl+++Ns+n++ri +q+ +++++ +e + +      +++ ++vpsgnfg++l ++++kk + 
  NCBI__GCF_000186245.1:WP_013553364.1 212 TfreelrkrDLKLSAANSVNFGRIIFQIiYHIHSYLELVRQnviTLGEEIYLVVPSGNFGNALGAYYAKKAG- 283
                                           456778888******************************996666789*******************99999. PP

                             TIGR00260 209 lpieklaiaaegaadivrrflksg.dlepkedk.eTlstAmdignpsnverale...larrslgnledlke.. 274
                                           lp++k+ ia++ + +i++  +++g +++  + + +T s+Amdi+++snver+l    + +r+ + +e+l +  
  NCBI__GCF_000186245.1:WP_013553364.1 284 LPVRKILIASNAN-NILTDWIRKGeYDLRGRCLiQTESPAMDILISSNVERVLYdkfGPERTRELMEALSKeg 355
                                           ***********98.99999999995666656558******************9888899**********889* PP

                             TIGR00260 275 ..................svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFe 325
                                                             + s++e  e+i   ++e+gyl++phta+ ++a ++l  +      ++ta+  KF+
  NCBI__GCF_000186245.1:WP_013553364.1 356 hysltpeelkslqedfdaTFSSDEEGEKIIARYAERGYLMDPHTATCLKAYRELRREPlatvIYSTAEWTKFS 428
                                           ******************99*********************************99988876666********* PP

                             TIGR00260 326 evvealtg 333
                                           ++v++  g
  NCBI__GCF_000186245.1:WP_013553364.1 429 RTVARAIG 436
                                           ***96555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (488 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: 00:00:00.02
# Mc/sec: 6.23
//
[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:

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