Alignments for a candidate for thrC in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Chlorobaculum tepidum TLS

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate NP_662910.1 CT2035 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>NCBI__GCF_000006985.1:NP_662910.1
          Length = 441

 Score =  333 bits (854), Expect = 6e-96
 Identities = 182/416 (43%), Positives = 254/416 (61%), Gaps = 9/416 (2%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           M  Y+    +  V+  +A  +GL  + GL+ P  +P FS  EI  +    F   +  +  
Sbjct: 1   MIFYSTTKASAPVTMKKATLEGLAPDGGLYVPSTMPHFSAEEIALLENGSFNNIAFAVAK 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
            F GDEIP + L E +   F F  P+  ++ D    ELFHGPTLAFKD+G RF+A+M  +
Sbjct: 61  KFAGDEIPLDRLSELIDECFTFDTPLHELDPDTFVEELFHGPTLAFKDYGARFLARMTGY 120

Query: 121 IAGDKP--VTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIE 178
            A ++   +T+L ATSGDTG+AVA+ F+G+PN +VV+LYP GK+S LQE+   T G N+ 
Sbjct: 121 FAAEESRLITVLVATSGDTGSAVAYGFHGIPNTRVVLLYPSGKVSRLQEQQLTTAGDNVF 180

Query: 179 TVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETR 238
            + + GDFD CQ LVKQAF D+ L+  L L SANSINISRL+ Q  YY  A  QL Q   
Sbjct: 181 ALEVKGDFDDCQRLVKQAFVDQSLRQKLTLTSANSINISRLIPQSFYYAWAALQLRQRKP 240

Query: 239 NQL-VVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATL 297
           + L + SVPSGN+G+LTAG++AK +G P+  FIAA+N ND+V R+L +G++ PK T  TL
Sbjct: 241 DALPIFSVPSGNYGNLTAGVMAKMMGFPIGHFIAASNANDSVTRYLDEGRYEPKPTVRTL 300

Query: 298 SNAMDVSQPNNWPRVEELFRRKIWQL-KELGYAAVDDETTQQTMRELKE-LGYTSEPHAA 355
           + AMDV  P+N+ R+   F     ++ +E+   AV D  T +T+R + E  GY  +PH A
Sbjct: 301 TTAMDVGNPSNFARLRYFFENDFRKMGQEITGIAVSDAETLETIRSVYEKYGYVMDPHTA 360

Query: 356 VAYRAL----RDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLP 407
           V YRAL    +D    G  G+ L TAHP KF E+++   G  + LP+ + E    P
Sbjct: 361 VGYRALDRFRQDHAGAGTPGVVLSTAHPVKFDEAIKEATGNEVPLPETMEEIMSKP 416


Lambda     K      H
   0.319    0.135    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: 449
Number of extensions: 15
Number of successful extensions: 5
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: 428
Length of database: 441
Length adjustment: 32
Effective length of query: 396
Effective length of database: 409
Effective search space:   161964
Effective search space used:   161964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate NP_662910.1 CT2035 (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.8633.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    5.9e-89  284.5   0.0    7.4e-89  284.2   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_662910.1  CT2035 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_662910.1  CT2035 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.2   0.0   7.4e-89   7.4e-89      12     339 ..      66     406 ..      58     407 .. 0.90

  Alignments for each domain:
  == domain 1  score: 284.2 bits;  conditional E-value: 7.4e-89
                              TIGR00260  12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAts 81 
                                            e++l  l e   e f+++++ +e+   + +v elfhgPtlaFKD g +f+a +  +++ +     tvl+Ats
  lcl|NCBI__GCF_000006985.1:NP_662910.1  66 EIPLDRLSELIDECFTFDTPLHELDP-DTFVEELFHGPTLAFKDYGARFLARMTGYFAAEESRliTVLVATS 136
                                            5677888999999************9.****************************9998888778******* PP

                              TIGR00260  82 GdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...kl 150
                                            Gdtg+a+a+++ g +n +vv LyP+gk+s ++e+ +t+   n+  l++kGdFDd+q+lvk++f d+    kl
  lcl|NCBI__GCF_000006985.1:NP_662910.1 137 GDTGSAVAYGFHGIPNTRVVLLYPSGKVSRLQEQQLTTAGDNVFALEVKGDFDDCQRLVKQAFVDQSlrqKL 208
                                            *******************************99999***************************9655566** PP

                              TIGR00260 151 klnsvNsinparieaqk.tyafeiveqlgkespdkv.vvpvpsgnfgailkGflekkelglpieklaiaaeg 220
                                             l s+Nsin++r+  q  +ya+ +++  + ++pd + +++vpsgn g++++G + +k++g p    +iaa +
  lcl|NCBI__GCF_000006985.1:NP_662910.1 209 TLTSANSINISRLIPQSfYYAWAALQLRQ-RKPDALpIFSVPSGNYGNLTAG-VMAKMMGFP-IGHFIAASN 277
                                            *****************9****9997665.788887589*************.6777777**.678899999 PP

                              TIGR00260 221 aadivrrflksgdlepkedkeTlstAmdignpsnverale....larrslgnledlkesvsdeeileaikkl 288
                                            a+d v+r+l +g  epk ++ Tl tAmd+gnpsn+ r+       +r+ +++++ +  +vsd+e+le+i+ +
  lcl|NCBI__GCF_000006985.1:NP_662910.1 278 ANDSVTRYLDEGRYEPKPTVRTLTTAMDVGNPSNFARLRYffenDFRKMGQEITGI--AVSDAETLETIRSV 347
                                            99***********************************9983334455555555655..************** PP

                              TIGR00260 289 aeeegyllephtavavaalkklvekg..vs......atadpaKFeevvealtgnklkdp 339
                                            +e+ gy+++phtav+++al +  ++    +      +ta+p KF e++   tgn+   p
  lcl|NCBI__GCF_000006985.1:NP_662910.1 348 YEKYGYVMDPHTAVGYRALDRFRQDHagAGtpgvvlSTAHPVKFDEAIKEATGNEVPLP 406
                                            *******************99888775522556778*****************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (441 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: 00:00:00.01
# Mc/sec: 9.31
//
[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