Alignments for a candidate for thrC in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Sphingomonas wittichii RW1

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011952255.1 SWIT_RS07155 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000016765.1:WP_011952255.1
          Length = 466

 Score =  474 bits (1220), Expect = e-138
 Identities = 245/458 (53%), Positives = 312/458 (68%), Gaps = 1/458 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+YVSTRG AP LGF D  LAGLA DGGLY+P+++P F+  +I ALRG SYV+ A+AV+ 
Sbjct: 1   MQYVSTRGSAPRLGFEDVTLAGLAADGGLYVPEQWPVFSTAEIAALRGLSYVDTAVAVMK 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF  G +  A+ + +   AYG F H AV PL Q D  ++++ELFHGPTLAFKDVA+QLL 
Sbjct: 61  PFVAGALDDAELKELCEAAYGRFAHAAVVPLKQLDHRQWLMELFHGPTLAFKDVALQLLG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
            + +  LA+R    T++GATSGDTG AAI+A  GR   DIF+L P GRVS VQ+RQMT+ 
Sbjct: 121 LLFERFLAKRDTHLTVIGATSGDTGSAAIDALAGRAKVDIFMLHPKGRVSEVQRRQMTTV 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
              NVH ++IEG+FDD Q LVK MF D +F    +LS VNSINWAR+M QVVYYF AA+ 
Sbjct: 181 LAPNVHNIAIEGSFDDAQALVKAMFADADFAGRFNLSAVNSINWARLMAQVVYYFYAAVR 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAPDR V+F+VPTGNFGD+FAGYVA RMGLP+ +LI+ATN NDIL R L +G Y +  V
Sbjct: 241 LGAPDRPVAFSVPTGNFGDVFAGYVAARMGLPVARLIVATNVNDILHRALSAGDYSVGTV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             T +PSMDIQ+SSNFERLLF+ HGRD AA    M+G + S    I     +     FS+
Sbjct: 301 TPTAAPSMDIQVSSNFERLLFDLHGRDGAATAATMEGFEASRRLDIPATMRAEAAGLFSS 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREK-ASGTAPMVVLATAHPAKFPDAV 419
            R   D     +     +    +DPHSAIG+  A++     + P+V LATAHPAKF DAV
Sbjct: 361 ARIDADRMQIAMRWAHDRAVETIDPHSAIGLAAAQDSDLDPSIPIVTLATAHPAKFGDAV 420

Query: 420 KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYV 457
           + A G  P LPA + +L +R+E + VL  E+  +E +V
Sbjct: 421 ERATGTRPTLPARIGELFERQERYAVLPAEIGAIEGFV 458


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: 580
Number of extensions: 21
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: 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 WP_011952255.1 SWIT_RS07155 (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.3892.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.4e-78  248.8   0.0    6.1e-78  248.3   0.0    1.1  1  lcl|NCBI__GCF_000016765.1:WP_011952255.1  SWIT_RS07155 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_011952255.1  SWIT_RS07155 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.3   0.0   6.1e-78   6.1e-78      12     334 ..      69     426 ..      59     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 248.3 bits;  conditional E-value: 6.1e-78
                                 TIGR00260  12 ekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tv 76 
                                               +++l++l+e  +  f+  ++   +++   + ++ elfhgPtlaFKD++lq ++ l++++l +  +  tv
  lcl|NCBI__GCF_000016765.1:WP_011952255.1  69 DAELKELCEAAYGRFAHAAVVplKQLDH-RQWLMELFHGPTLAFKDVALQLLGLLFERFLAKRDThlTV 136
                                               6788999999999999888877788888.99***************************998777777** PP

                                 TIGR00260  77 lcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeif 144
                                               ++AtsGdtg+aa+ alag+a v++++L Pkg++s v   +++t+la n++ +ai+G FDdaq+lvk++f
  lcl|NCBI__GCF_000016765.1:WP_011952255.1 137 IGATSGDTGSAAIDALAGRAKVDIFMLHPKGRVSEVqRRQMTTVLAPNVHNIAIEGSFDDAQALVKAMF 205
                                               ************************************99******************************* PP

                                 TIGR00260 145 edke...klklnsvNsinparieaqktyafeiveqlgkespdk.vvvpvpsgnfgailkGflekkelgl 209
                                                d       +l++vNsin+ar+ aq++y+f ++ +lg  +pd+ v+++vp gnfg++++G+++++++ l
  lcl|NCBI__GCF_000016765.1:WP_011952255.1 206 ADADfagRFNLSAVNSINWARLMAQVVYYFYAAVRLG--APDRpVAFSVPTGNFGDVFAGYVAARMG-L 271
                                               97666899******************99999999999..555449*********************9.* PP

                                 TIGR00260 210 pieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke... 274
                                               p++ l +a++  +di++r l  gd +  +   T +++mdi  +sn+er+l+ l  r ++   +      
  lcl|NCBI__GCF_000016765.1:WP_011952255.1 272 PVARLIVATNV-NDILHRALSAGDYSVGTVTPTAAPSMDIQVSSNFERLLFdLHGRDGAATAAT-Megf 338
                                               *7666666665.5**********88888888********************6555554444444.3489 PP

                                 TIGR00260 275 ......................svsdeeileaikklaeeegy.llephtavavaalkkl.vekg...vs 316
                                                                     +  d++ ++  ++ a+ + + +++ph+a+++aa ++  ++ +   v+
  lcl|NCBI__GCF_000016765.1:WP_011952255.1 339 easrrldipatmraeaaglfssARIDADRMQIAMRWAHDRAVeTIDPHSAIGLAAAQDSdLDPSipiVT 407
                                               99****************999866677777766666666554389*********999862555577633 PP

                                 TIGR00260 317 .atadpaKFeevvealtgn 334
                                                ata+paKF ++ve+ tg 
  lcl|NCBI__GCF_000016765.1:WP_011952255.1 408 lATAHPAKFGDAVERATGT 426
                                               7*************99996 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.10
//
[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