Alignments for a candidate for thrC in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Marinobacter adhaerens HP15

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate GFF786 HP15_765 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__Marino:GFF786
          Length = 466

 Score =  484 bits (1245), Expect = e-141
 Identities = 249/463 (53%), Positives = 316/463 (68%), Gaps = 4/463 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+Y+STRGEAP LGF D LL GLA DGGLY+P+  P F  E+IR+ RG SY E+A  V+ 
Sbjct: 1   MRYISTRGEAPALGFEDVLLTGLATDGGLYVPESLPHFDLEEIRSWRGLSYSELAFNVMY 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF    IPA DF +M+ E Y  F H AV PLVQ D NE+V+ELF GPTLAFKD A+QLL 
Sbjct: 61  PFVDDAIPADDFRKMLDETYSVFAHKAVAPLVQLDTNEWVMELFRGPTLAFKDFALQLLG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R++DYVL +R +   I+GATSGDTG AAIE     ++ DIFIL P  RVS VQ+RQMT+ 
Sbjct: 121 RLLDYVLEKRKQHVVIMGATSGDTGSAAIEGCRRCEHVDIFILHPYQRVSEVQRRQMTTV 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDA-LSLSGVNSINWARIMPQVVYYFTAAL 239
              N+H +++ GNFDDCQ +VK  F +  F      L+ VNSINWARIM Q+VYYF A+L
Sbjct: 181 QGENIHNIAVRGNFDDCQRMVKESFGNQSFLGGKTQLAAVNSINWARIMAQIVYYFHASL 240

Query: 240 SLGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRG 299
           +LG PDR+++F+VPTGNFGDIFAGY+AK+MGLPI QL+IATN NDIL R +    YE   
Sbjct: 241 ALGGPDRSMAFSVPTGNFGDIFAGYLAKKMGLPISQLVIATNRNDILHRFMSGNKYEQHQ 300

Query: 300 VAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFS 359
           +  T SPSMDI +SSNFERLLF+ HGRD  AV+ L++   + G  +I +      R  F 
Sbjct: 301 LEHTLSPSMDIMVSSNFERLLFDLHGRDGLAVKTLLENAAK-GPVSIEDYRWKHARKLFD 359

Query: 360 AGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE-KASGTAPMVVLATAHPAKFPDA 418
           +       T  TI  +  ++ YLLDPH+AIGV+ AR  +     PM+ L TAHPAKFPDA
Sbjct: 360 SDAVDDKATCDTIREIYEQNEYLLDPHTAIGVRAARNCRRDQAVPMITLGTAHPAKFPDA 419

Query: 419 V-KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460
           V ++   VEP LPA + DL +R+E +TVL N +  V+ ++  H
Sbjct: 420 VAESGVSVEPPLPAHMADLFEREERYTVLDNNIDGVQAFIAKH 462


Lambda     K      H
   0.320    0.135    0.389 

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: 551
Number of extensions: 24
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: 463
Length of database: 466
Length adjustment: 33
Effective length of query: 430
Effective length of database: 433
Effective search space:   186190
Effective search space used:   186190
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 GFF786 HP15_765 (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.17440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    3.7e-86  275.3   0.0    5.2e-86  274.8   0.0    1.1  1  lcl|FitnessBrowser__Marino:GFF786  HP15_765 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF786  HP15_765 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.8   0.0   5.2e-86   5.2e-86      15     329 ..      72     421 ..      62     425 .. 0.93

  Alignments for each domain:
  == domain 1  score: 274.8 bits;  conditional E-value: 5.2e-86
                          TIGR00260  15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaa 87 
                                          ++    +++f+ +++a  v++  n +v elf gPtlaFKD++lq ++ ll ++le+ ++  ++++AtsGdtg+a
  lcl|FitnessBrowser__Marino:GFF786  72 FRKMLDETYSVFAHKAVAPLVQLdTNEWVMELFRGPTLAFKDFALQLLGRLLDYVLEKRKQhvVIMGATSGDTGSA 147
                                        55566778999999999988888889*******************************99988899*********** PP

                          TIGR00260  88 aaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke....klklnsvNsi 158
                                        a+e+ ++ + v++++L P  ++s v   +++t+  en++ +a++G+FDd+q++vke f+++     k++l +vNsi
  lcl|FitnessBrowser__Marino:GFF786 148 AIEGCRRCEHVDIFILHPYQRVSEVqRRQMTTVQGENIHNIAVRGNFDDCQRMVKESFGNQSflggKTQLAAVNSI 223
                                        *************************99********************************7777999********** PP

                          TIGR00260 159 nparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdl 234
                                        n+ari aq++y+f +  +lg+ ++  ++++vp gnfg+i++G+l+kk++ lpi  l ia++ + di++rf+ + + 
  lcl|FitnessBrowser__Marino:GFF786 224 NWARIMAQIVYYFHASLALGGPDR-SMAFSVPTGNFGDIFAGYLAKKMG-LPISQLVIATNRN-DILHRFMSGNKY 296
                                        ********************6554.689********************9.************9.******888888 PP

                          TIGR00260 235 epkedkeTlstAmdignpsnverale.larrslgnledlke........................svsdeeileai 285
                                        e+++  +Tls++mdi  +sn+er+l+ l  r +  ++ l e                        +v d+++ ++i
  lcl|FitnessBrowser__Marino:GFF786 297 EQHQLEHTLSPSMDIMVSSNFERLLFdLHGRDGLAVKTLLEnaakgpvsiedyrwkharklfdsdAVDDKATCDTI 372
                                        888888*******************988888888888886689********************************* PP

                          TIGR00260 286 kklaeeegyllephtavavaalkklvekg...vs..atadpaKFeevve 329
                                        ++++e+++yll+phta++v+a ++   ++   +   +ta+paKF+++v+
  lcl|FitnessBrowser__Marino:GFF786 373 REIYEQNEYLLDPHTAIGVRAARNCRRDQavpMItlGTAHPAKFPDAVA 421
                                        **********************99998887651157**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (466 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: 11.85
//
[ok]

This GapMind analysis is from Apr 09 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