Alignments for a candidate for thrC in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Hydrogenovibrio halophilus DSM 15072

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_019896357.1 A377_RS0110705 threonine synthase

Query= curated2:O24924
         (486 letters)



>NCBI__GCF_000384235.1:WP_019896357.1
          Length = 494

 Score =  390 bits (1003), Expect = e-113
 Identities = 221/494 (44%), Positives = 301/494 (60%), Gaps = 13/494 (2%)

Query: 1   MPFVPTRS---LKEKKIDFIEAILNPNAPKGGLYTLERFETLQW---QDCLNLSYNDLVE 54
           M F+ TR     +  K  F +AIL+P +  GGLY+ E    L     Q  +   Y  L  
Sbjct: 1   MNFIETRGNDGQRPPKFTFSQAILSPMSSFGGLYSPESLPDLGLPFLQAHIQSDYQTLAT 60

Query: 55  CVFERLGLEIPKNLLASALKRYENFDNPKNPAPIFALNERLFVQELYHGPSLAFKDMALQ 114
            + +   ++I  +++A A+ RY +FD P NP P+  L + L+V EL+HGP+ AFKDMALQ
Sbjct: 61  AILDAFEVDIDPDVIAQAVGRYNDFDEPTNPVPVVKLYDDLYVSELFHGPTRAFKDMALQ 120

Query: 115 PLASLFSNLAVGKNEKYLMLVSTSGDTGPATLESLAGMPNVFVVCLYPKDGTSLVQKLQM 174
           P   + S +A  + EK+L+L +TSGDTGPA LE+     +V V CLYP  GTS VQ+LQM
Sbjct: 121 PFGQVLSAVAEQRQEKFLILAATSGDTGPAALETFKARSHVQVACLYPDGGTSDVQRLQM 180

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

Query: 235 YHIWGFLELYKKGAINSKEKITLAIPSGNFGNALGAFYAKKMGLNIDKIKVVTNSNDVLR 294
           YH++ +L L ++ AI   EK+ L +PSGNFGNALG +YA KMGL +++I + +N N+VL 
Sbjct: 241 YHLYSYLALVRQNAITMGEKVYLNVPSGNFGNALGGYYAYKMGLPVEQIHIASNQNNVLT 300

Query: 295 EFIETGRYDLTHRSLKQTYSPAMDILKSSNVERALFSLFGFERTLELMQALEEEKFYALK 354
            FIETG YDL +R +  T SPAMDILKSSN+ER LF LFG ERT ELM+ L+ E  Y L 
Sbjct: 301 RFIETGCYDLRNRDVIPTTSPAMDILKSSNIERILFDLFGPERTRELMEQLDREDHYQLS 360

Query: 355 PKELALLQEHFSCASCSDEACLKTIQEVYAEHQYLIDPHTATALNASLKTHEK----TLV 410
             ELA +Q  F+   CSD      I++ + +  YL+ PHTAT L       +     T+ 
Sbjct: 361 DAELAQVQAIFAADYCSDSEGKAYIKQAFEQKGYLMCPHTATCLKPYQTQRQDPSLVTIA 420

Query: 411 SATASYEKFPRITLLAL-NEQKKNDNDKAALETLKNSYNTPDSQRLDDLFERGIKHQEVL 469
            +TA + KF  I   AL  E  ++D D  AL+ +        S ++  LFE  +  + ++
Sbjct: 421 YSTAEWTKFSTIIAEALTGEHYQHDVD--ALKAVSELSGAAISSQISRLFELPVTQKTII 478

Query: 470 KLNEIKSSILLWLE 483
              EI+ +IL +L+
Sbjct: 479 DKAEIEPTILAFLK 492


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: 529
Number of extensions: 16
Number of successful extensions: 2
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: 494
Length adjustment: 34
Effective length of query: 452
Effective length of database: 460
Effective search space:   207920
Effective search space used:   207920
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_019896357.1 A377_RS0110705 (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.27077.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.9e-88  282.2   0.0      4e-88  281.8   0.0    1.1  1  lcl|NCBI__GCF_000384235.1:WP_019896357.1  A377_RS0110705 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384235.1:WP_019896357.1  A377_RS0110705 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.0     4e-88     4e-88       9     335 ..      67     441 ..      60     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 4e-88
                                 TIGR00260   9 evt.ekdlvdlaegstelfrspklaeevga..enlyvkelfhgPtlaFKDrglqfvavlltkalelgne 74 
                                               ev  + d+++ a g+++ f+ p+++ +v +   +lyv elfhgPt aFKD++lq+ +++l++++e+ +e
  lcl|NCBI__GCF_000384235.1:WP_019896357.1  67 EVDiDPDVIAQAVGRYNDFDEPTNPVPVVKlyDDLYVSELFHGPTRAFKDMALQPFGQVLSAVAEQRQE 135
                                               5666789999999************99988899*********************************999 PP

                                 TIGR00260  75 ..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlv 140
                                                 ++l AtsGdtg+aa+e +++++ v+v +LyP+g++s v   ++vt  a n+kv++ikGdFDdaq+++
  lcl|NCBI__GCF_000384235.1:WP_019896357.1 136 kfLILAATSGDTGPAALETFKARSHVQVACLYPDGGTSDVqRLQMVTEAADNLKVIGIKGDFDDAQTAL 204
                                               99**************************************99*************************** PP

                                 TIGR00260 141 keifedke........klklnsvNsinparieaqk.tyafeiveqlgk...espdkvvvpvpsgnfgai 197
                                               k+++  +          + l+++Ns+n++ri +q  ++ ++ ++ + +      +kv + vpsgnfg++
  lcl|NCBI__GCF_000384235.1:WP_019896357.1 205 KKLLTSDTfrqtledqDIYLSAANSVNFGRIIFQTiYHLYSYLALVRQnaiTMGEKVYLNVPSGNFGNA 273
                                               ****9544577788889*****************99********99995556689************** PP

                                 TIGR00260 198 lkGflekkelglpieklaiaaegaadivrrflksg.dlepkedk.eTlstAmdignpsnverale...l 261
                                               l G++++k++ lp+e + ia++++ ++++rf+++g +++  +d+  T s+Amdi+++sn+er+l+   +
  lcl|NCBI__GCF_000384235.1:WP_019896357.1 274 LGGYYAYKMG-LPVEQIHIASNQN-NVLTRFIETGcYDLRNRDViPTTSPAMDILKSSNIERILFdlfG 340
                                               **********.************9.**********9999999989*******************99777 PP

                                 TIGR00260 262 arrslgnledlke.....................svsdeeileaikklaeeegyllephtavavaalkk 309
                                                +r+ + +e+l+                       +sd+e    ik++ e++gyl+ phta+ ++  + 
  lcl|NCBI__GCF_000384235.1:WP_019896357.1 341 PERTRELMEQLDRedhyqlsdaelaqvqaifaadYCSDSEGKAYIKQAFEQKGYLMCPHTATCLKPYQT 409
                                               79*********889****************************************************999 PP

                                 TIGR00260 310 lvekg.....vsatadpaKFeevve.altgnk 335
                                               + ++       ++ta+  KF+++++ altg++
  lcl|NCBI__GCF_000384235.1:WP_019896357.1 410 QRQDPslvtiAYSTAEWTKFSTIIAeALTGEH 441
                                               998777866556*************9****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (494 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: 11.01
//
[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