Alignments for a candidate for thrC in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Hydrogenovibrio marinus DSM 11271

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_029909039.1 P166_RS0104155 threonine synthase

Query= curated2:O24924
         (486 letters)



>NCBI__GCF_000711315.1:WP_029909039.1
          Length = 491

 Score =  405 bits (1041), Expect = e-117
 Identities = 225/492 (45%), Positives = 310/492 (63%), Gaps = 12/492 (2%)

Query: 1   MPFVPTRSLKEKK---IDFIEAILNPNAPKGGLYT---LERFETLQWQDCLNLSYNDLVE 54
           M F+ TR    ++   I F +AIL+P +  GG+Y+   L  F+   +   +N  Y  L +
Sbjct: 1   MKFIETRGNDGQRPTHISFAQAILSPMSSFGGIYSPESLPSFDEAFFMSHVNSGYKTLAK 60

Query: 55  CVFERLGLEIPKNLLASALKRYENFDNPKNPAPIFALNERLFVQELYHGPSLAFKDMALQ 114
            V +   ++I + ++  AL  Y+ FD+P NP P+  + + LFV ELYHGP+ AFKDMALQ
Sbjct: 61  DVLKAFEIDIEEKIIDEALALYDEFDDPSNPVPVVKVYDDLFVSELYHGPTRAFKDMALQ 120

Query: 115 PLASLFSNLAVGKNEKYLMLVSTSGDTGPATLESLAGMPNVFVVCLYPKDGTSLVQKLQM 174
           P   + S LA  ++EKYL+L +TSGDTGPA LE+     NV V CLYP  GTS VQ+LQM
Sbjct: 121 PFGKVLSALAQARDEKYLILAATSGDTGPAALETFKNRDNVQVACLYPDGGTSDVQRLQM 180

Query: 175 VTQSASNLKVFGISGDFDDAQNALKNLLKDDDFNEALKACQLKLSVANSVNFGRIAFQIV 234
           VT+ A+NLKV GI GDFDDAQ ALK+LL  + F +ALK   + LS ANSVNFGRI FQ +
Sbjct: 181 VTEDAANLKVIGIHGDFDDAQTALKSLLVSEKFRDALKEHNISLSAANSVNFGRIIFQTI 240

Query: 235 YHIWGFLELYKKGAINSKEKITLAIPSGNFGNALGAFYAKKMGLNIDKIKVVTNSNDVLR 294
           YHI+ +LEL ++GAI   +++ L +PSGNFGNALG +YA KMGL + +I + +N N+VL 
Sbjct: 241 YHIYSYLELVRQGAIQMGDQVYLNVPSGNFGNALGGYYALKMGLPVKQIHIASNMNNVLT 300

Query: 295 EFIETGRYDLTHRSLKQTYSPAMDILKSSNVERALFSLFGFERTLELMQALEEEKFYALK 354
           +FI TGRYDL   S+  T SPAMDILKSSN+ER LF LFG ERT ELM  L+  KFY L 
Sbjct: 301 KFINTGRYDLREISVIPTTSPAMDILKSSNIERVLFDLFGAERTKELMFELDNHKFYELT 360

Query: 355 PKELALLQEHFSCASCSDEACLKTIQEVYAEHQYLIDPHTATALNASLKTHE----KTLV 410
             EL+ +Q  F+   C+DE  +  IQ+ ++   YL+ PHTAT   A     E    KT+ 
Sbjct: 361 EAELSQVQAIFAADFCTDEEGMNYIQQAFSV-GYLMCPHTATCFKAYDTCREDKTLKTIA 419

Query: 411 SATASYEKFPRITLLALNEQKKNDNDKAALETLKNSYNTPDSQRLDDLFERGIKHQEVLK 470
            +TA + KF  +   AL      ++D+ AL+ + +        +++ LF + +  + V+ 
Sbjct: 420 YSTAEWTKFSPVIAKALTGD-IYEHDRDALKMIADKAGISIPSQIEALFSKPVAQKTVID 478

Query: 471 LNEIKSSILLWL 482
             +I+S IL +L
Sbjct: 479 KQDIESEILKFL 490


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: 573
Number of extensions: 24
Number of successful extensions: 3
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: 491
Length adjustment: 34
Effective length of query: 452
Effective length of database: 457
Effective search space:   206564
Effective search space used:   206564
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_029909039.1 P166_RS0104155 (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.20116.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.2e-83  264.1   0.0    1.2e-82  263.7   0.0    1.1  1  lcl|NCBI__GCF_000711315.1:WP_029909039.1  P166_RS0104155 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711315.1:WP_029909039.1  P166_RS0104155 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.7   0.0   1.2e-82   1.2e-82       8     334 ..      66     439 ..      60     444 .. 0.93

  Alignments for each domain:
  == domain 1  score: 263.7 bits;  conditional E-value: 1.2e-82
                                 TIGR00260   8 levt.ekdlvdlaegstelfrspklaeevga..enlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 
                                                e+  e++++d a   +  f+ p ++ +v +   +l+v el+hgPt aFKD++lq+ +++l++++++  
  lcl|NCBI__GCF_000711315.1:WP_029909039.1  66 FEIDiEEKIIDEALALYDEFDDPSNPVPVVKvyDDLFVSELYHGPTRAFKDMALQPFGKVLSALAQARD 134
                                               5666688889999999999****99998888899*******************************9998 PP

                                 TIGR00260  74 e..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdl 139
                                               e  ++l AtsGdtg+aa+e ++ + nv+v +LyP+g++s v   ++vt  a n+kv++i+GdFDdaq++
  lcl|NCBI__GCF_000711315.1:WP_029909039.1 135 EkyLILAATSGDTGPAALETFKNRDNVQVACLYPDGGTSDVqRLQMVTEDAANLKVIGIHGDFDDAQTA 203
                                               888**************************************99************************** PP

                                 TIGR00260 140 vkeife.dke........klklnsvNsinparieaqk.tyafeiveqlgk...espdkvvvpvpsgnfg 195
                                               +k+++  + +        ++ l+++Ns+n++ri +q  +++++ +e + +   +  d+v + vpsgnfg
  lcl|NCBI__GCF_000711315.1:WP_029909039.1 204 LKSLLVsE-KfrdalkehNISLSAANSVNFGRIIFQTiYHIYSYLELVRQgaiQMGDQVYLNVPSGNFG 271
                                               ***99844.4488888889*****************99*********99999999************** PP

                                 TIGR00260 196 ailkGflekkelglpieklaiaaegaadivrrflksg..dlepkedkeTlstAmdignpsnverale.. 260
                                               ++l G++++k++ lp++ + ia++ + +++++f+++g  dl +++   T s+Amdi+++sn+er+l+  
  lcl|NCBI__GCF_000711315.1:WP_029909039.1 272 NALGGYYALKMG-LPVKQIHIASNMN-NVLTKFINTGryDLREISVIPTTSPAMDILKSSNIERVLFdl 338
                                               ************.************8.*********98566666777*******************999 PP

                                 TIGR00260 261 .larrslgnledlke.....................svsdeeileaikklaeeegyllephtavavaal 307
                                                +a+r+++ + +l++                      ++dee ++ i+++  + gyl+ phta+  +a 
  lcl|NCBI__GCF_000711315.1:WP_029909039.1 339 fGAERTKELMFELDNhkfyelteaelsqvqaifaadFCTDEEGMNYIQQAF-SVGYLMCPHTATCFKAY 406
                                               999**********99********************99*********99976.67**************9 PP

                                 TIGR00260 308 kklvekg.....vsatadpaKFeevve.altgn 334
                                                   e+       ++ta+  KF+ v++ altg 
  lcl|NCBI__GCF_000711315.1:WP_029909039.1 407 DTCREDKtlktiAYSTAEWTKFSPVIAkALTGD 439
                                               88887776765566************99**996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (491 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: 12.69
//
[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