Alignments for a candidate for thrC in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Clostridium kluyveri DSM 555

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011989272.1 CKL_RS03460 threonine synthase

Query= BRENDA::P16120
         (514 letters)



>NCBI__GCF_000016505.1:WP_011989272.1
          Length = 496

 Score =  270 bits (691), Expect = 7e-77
 Identities = 180/523 (34%), Positives = 284/523 (54%), Gaps = 48/523 (9%)

Query: 8   YRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAIMR 67
           Y STR  + K  +   AI+ G++ DGGLFIP TIP +D+  L      +++++LA  I+ 
Sbjct: 6   YNSTRGLN-KNFTASRAILNGISEDGGLFIPHTIPFIDEEEL-KKLKYMTYKELALCIIE 63

Query: 68  LYIAQEEIPDADLKDLIKRSYST-FRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDV 126
            +    +    +LK+ I  +Y   F SD++ PL +   GD   +  LELFHGPT AFKD+
Sbjct: 64  KFFT--DFSKEELKECIDLAYDNKFESDKIVPLEK--VGD---VFYLELFHGPTLAFKDM 116

Query: 127 ALQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPT 186
           AL  + +L +   ++   +      K+I ++ ATSGDTG AA+ G    +   + + +P 
Sbjct: 117 ALCLLPHLMKTAAKKQKLH------KEIVILTATSGDTGKAALEGFANVEGTKIVVFFPE 170

Query: 187 GRISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFNSKHN-----VGAVNS 241
             +S IQ++QM T    N + + + G FD+ Q  VK IF D E   + N       + NS
Sbjct: 171 QGVSKIQKKQMVTQQGGNTKVVGIEGNFDDAQSEVKKIFNDHELKEELNENSYRFSSANS 230

Query: 242 INWARILAQMTYYFYSFFQATNGKD---SKKVKFVVPSGNFGDILAGYFAKKMGLPIEKL 298
           IN  R++ Q+ YYFY + +     +     K+ F VP+GNFG+ILA Y+AKKMGLPI KL
Sbjct: 231 INIGRLIPQVVYYFYGYMELLRRGEINFGNKINFSVPTGNFGNILAAYYAKKMGLPINKL 290

Query: 299 AIATNENDILDRFLKSGLYERSDKVAATLSPAMDILISSNFERLLWYLAREYLANGDDLK 358
             A+NEN +L  F ++G Y+   +   T+SP+MDILISSN ERL++ ++          K
Sbjct: 291 ICASNENRVLYDFFENGTYDAEREFILTISPSMDILISSNLERLIYDISG---------K 341

Query: 359 AGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYI 418
              +VN     L  + K+ V +S+ E   K F     S EET + IK+ +++      Y+
Sbjct: 342 DSTVVNKLMTNLSEHSKYTVSESMKE-ELKVFYGGFASEEETLKCIKETFDT----YQYL 396

Query: 419 LDPHTAVGVCATERLIAKDNDKSIQYISLSTAHPAKFADAVNNALSGFSNYSFEKDV-LP 477
           +D HT+V     +  + +D     + I +STA P KF  +V +AL   + YS+++D+ L 
Sbjct: 397 MDTHTSVAYSVYKNYL-RDTCDDTKTIVVSTASPFKFTKSVMSALD--TKYSYQEDLELV 453

Query: 478 EELKKLSTLKKKLKFIERADVELVKNAI------EEELAKMKL 514
           E + K+++L+      +  D ++V N +      +EE+ K  L
Sbjct: 454 EVMSKIASLEIPAPIRKLEDSKVVHNTVCKREEMKEEIRKFLL 496


Lambda     K      H
   0.316    0.133    0.374 

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: 635
Number of extensions: 38
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 514
Length of database: 496
Length adjustment: 34
Effective length of query: 480
Effective length of database: 462
Effective search space:   221760
Effective search space used:   221760
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: 52 (24.6 bits)

Align candidate WP_011989272.1 CKL_RS03460 (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.27416.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.8e-79  252.2   0.6    4.9e-79  251.9   0.6    1.1  1  lcl|NCBI__GCF_000016505.1:WP_011989272.1  CKL_RS03460 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_011989272.1  CKL_RS03460 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.9   0.6   4.9e-79   4.9e-79      24     332 ..      84     441 ..      64     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: 251.9 bits;  conditional E-value: 4.9e-79
                                 TIGR00260  24 elfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne....tvlcAtsGdtga 86 
                                               + f+s+k+   e+vg   ++ +elfhgPtlaFKD++l  +  l++ a+++++     ++l+AtsGdtg 
  lcl|NCBI__GCF_000016505.1:WP_011989272.1  84 NKFESDKIVplEKVGD--VFYLELFHGPTLAFKDMALCLLPHLMKTAAKKQKLhkeiVILTATSGDTGK 150
                                               5688888876677776..*******************99999998887766556788************ PP

                                 TIGR00260  87 aaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...... 148
                                               aa+e++a  ++ k+vv+ P+ ++s + k+++vt+  +n kv++i+G+FDdaq  vk+if+d+e      
  lcl|NCBI__GCF_000016505.1:WP_011989272.1 151 AALEGFANVEGTKIVVFFPEQGVSKIqKKQMVTQQGGNTKVVGIEGNFDDAQSEVKKIFNDHElkeeln 219
                                               ************************************************************777788999 PP

                                 TIGR00260 149 ..klklnsvNsinparieaqk.tyafeiveqlgk...espdkvvvpvpsgnfgailkGflekkelglpi 211
                                                  + ++s+Nsin++r+  q+ +y+++ +e l +   +  +k+ ++vp gnfg+il+++++kk++ lpi
  lcl|NCBI__GCF_000016505.1:WP_011989272.1 220 enSYRFSSANSINIGRLIPQVvYYFYGYMELLRRgeiNFGNKINFSVPTGNFGNILAAYYAKKMG-LPI 287
                                               99******************************99888999************************9.*** PP

                                 TIGR00260 212 eklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnverale.larrslgnledlke.... 274
                                               +kl  a++++  ++  f ++g ++ ++e   T+s++mdi+++sn er+   +  +    +++l +    
  lcl|NCBI__GCF_000016505.1:WP_011989272.1 288 NKLICASNEN-RVLYDFFENGtYDAEREFILTISPSMDILISSNLERLIYdISGKDSTVVNKLMTnlse 355
                                               *********9.9999999999677777777*****************9986655555555555446777 PP

                                 TIGR00260 275 ....................svsdeeileaikklaeeegyllephtavavaalkklvekg...vs.... 316
                                                                    +s+ee+l+ ik+   + +yl+++ht va+ + k+ + ++   +     
  lcl|NCBI__GCF_000016505.1:WP_011989272.1 356 hskytvsesmkeelkvfyggFASEEETLKCIKETFDTYQYLMDTHTSVAYSVYKNYLRDTcddTKtivv 424
                                               *******************999******************************99998888766224567 PP

                                 TIGR00260 317 atadpaKFeevve.alt 332
                                               +ta+p KF ++v+ al 
  lcl|NCBI__GCF_000016505.1:WP_011989272.1 425 STASPFKFTKSVMsALD 441
                                               ************96665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (496 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: 9.32
//
[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