Alignments for a candidate for thrC in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Geobacter lovleyi SZ

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012470330.1 GLOV_RS11290 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000020385.1:WP_012470330.1
          Length = 460

 Score =  412 bits (1060), Expect = e-120
 Identities = 213/436 (48%), Positives = 286/436 (65%), Gaps = 2/436 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+Y+STRG    + F DA++ GLA DGGL LP+  P F+A ++ + R  +Y ++A  +++
Sbjct: 1   MRYLSTRGGIAPVRFKDAVMMGLADDGGLLLPESIPAFSAAELESWRTLTYPQLAFKIIS 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
            F   +IPA D + ++  +Y TF H  V P+VQ D   ++LELFHG TLAFKDVA+Q L 
Sbjct: 61  RFVD-DIPATDLQALIDRSYATFSHPEVTPVVQKDG-VYILELFHGVTLAFKDVALQFLG 118

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
            + +Y+L +R ER TIVGATSGDTG AAI    G+    IFIL P+G+ SPVQ  QMTS 
Sbjct: 119 NLFEYILHERHERLTIVGATSGDTGSAAIHGVRGKAGISIFILHPHGKTSPVQALQMTSV 178

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
              NVH ++++G FDDCQ++VKG+  DLEF    SL  VNSINWAR++ QVVYY  A L 
Sbjct: 179 LDENVHNIAVDGTFDDCQDIVKGLMGDLEFKQKYSLGAVNSINWARVLAQVVYYIYAWLR 238

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           +    R V F+VPTGNFGDIFAGY+A++MGLP+E+L++ATN+N+IL+R +  G Y +  V
Sbjct: 239 VAEQGRKVVFSVPTGNFGDIFAGYMAQQMGLPVEKLLLATNENNILTRFINQGDYSVGTV 298

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
            QT SPSMDIQ++SNFER LF    +DAA V      LK  G  + S++ L  +R +F +
Sbjct: 299 VQTLSPSMDIQVASNFERYLFYLFKQDAARVSAAFAQLKAEGKISFSQQELQQVRQDFRS 358

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420
                  T  TI       GYLLDPH+A+GV+ A+E  +   P+V LATAHPAKF +AV 
Sbjct: 359 ASVDRQATLETIRQFKHDTGYLLDPHTAVGVRAAQELVTDDTPVVCLATAHPAKFGEAVV 418

Query: 421 AACGVEPQLPAWLCDL 436
            A G    +P  +  L
Sbjct: 419 EATGDAVPVPPAIAQL 434


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: 496
Number of extensions: 15
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: 463
Length of database: 460
Length adjustment: 33
Effective length of query: 430
Effective length of database: 427
Effective search space:   183610
Effective search space used:   183610
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 WP_012470330.1 GLOV_RS11290 (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.22076.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      1e-96  310.0   0.0    1.3e-96  309.7   0.0    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012470330.1  GLOV_RS11290 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012470330.1  GLOV_RS11290 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.7   0.0   1.3e-96   1.3e-96      11     334 ..      67     423 ..      59     428 .. 0.93

  Alignments for each domain:
  == domain 1  score: 309.7 bits;  conditional E-value: 1.3e-96
                                 TIGR00260  11 tekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvl 77 
                                               + +dl +l+ +s+++f  p+++  v++  +y++elfhg tlaFKD++lqf+++l++++l +  e  t++
  lcl|NCBI__GCF_000020385.1:WP_012470330.1  67 PATDLQALIDRSYATFSHPEVTPVVQKDGVYILELFHGVTLAFKDVALQFLGNLFEYILHERHErlTIV 135
                                               46899*******************************************************999999*** PP

                                 TIGR00260  78 cAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife 145
                                               +AtsGdtg+aa+++ +gka++++++L P+gk+spv + +++ +l+en++ +a++G+FDd+qd+vk +++
  lcl|NCBI__GCF_000020385.1:WP_012470330.1 136 GATSGDTGSAAIHGVRGKAGISIFILHPHGKTSPVqALQMTSVLDENVHNIAVDGTFDDCQDIVKGLMG 204
                                               ********************************************************************9 PP

                                 TIGR00260 146 ...dkeklklnsvNsinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglp 210
                                                   k+k+ l++vNsin+ar++aq+ +y++  +   +  +  kvv++vp gnfg+i++G+++ +++ lp
  lcl|NCBI__GCF_000020385.1:WP_012470330.1 205 dleFKQKYSLGAVNSINWARVLAQVvYYIYAWLRVAE--QGRKVVFSVPTGNFGDIFAGYMAQQMG-LP 270
                                               543455*******************999999988776..8899*****************999999.** PP

                                 TIGR00260 211 ieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.... 274
                                               +ekl  a++++ +i++rf+++gd +  + ++Tls++mdi   sn+er l+ l+++  + + +  +    
  lcl|NCBI__GCF_000020385.1:WP_012470330.1 271 VEKLLLATNEN-NILTRFINQGDYSVGTVVQTLSPSMDIQVASNFERYLFyLFKQDAARVSAAFAqlka 338
                                               **********9.**********99999999*******************99888887777666556777 PP

                                 TIGR00260 275 .....................svsdeeileaikklaeeegyllephtavavaalkklvekg..vs..at 318
                                                                    sv  +++le+i++  +  gyll+phtav+v+a ++lv ++  v   at
  lcl|NCBI__GCF_000020385.1:WP_012470330.1 339 egkisfsqqelqqvrqdfrsaSVDRQATLETIRQFKHDTGYLLDPHTAVGVRAAQELVTDDtpVVclAT 407
                                               ********************999999*********************************99773368** PP

                                 TIGR00260 319 adpaKFeevvealtgn 334
                                               a+paKF e+v+  tg 
  lcl|NCBI__GCF_000020385.1:WP_012470330.1 408 AHPAKFGEAVVEATGD 423
                                               **********988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (460 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: 14.13
//
[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