Alignments for a candidate for thrC in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Sinorhizobium meliloti 1021

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate SMc00077 SMc00077 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__Smeli:SMc00077
          Length = 466

 Score =  651 bits (1680), Expect = 0.0
 Identities = 326/462 (70%), Positives = 374/462 (80%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           +KY+STRGEA  LGF DALLAGLARDGGLYLP+E+P  + ++IRALRGKSY E+A  VL 
Sbjct: 2   VKYISTRGEAASLGFCDALLAGLARDGGLYLPKEWPALSKKEIRALRGKSYQEIAFTVLE 61

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PFT GEIPAA F  M+ EAY TFRH AV PLVQT  N FV+ELFHG TLAFKDVAMQLLA
Sbjct: 62  PFTNGEIPAAKFREMIDEAYATFRHPAVAPLVQTGPNAFVMELFHGSTLAFKDVAMQLLA 121

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R+MDYVLA+RGERATIVGATSGDTGGAAI+AF GRD TDIFILFP G+VSPVQQRQMT+S
Sbjct: 122 RLMDYVLAERGERATIVGATSGDTGGAAIDAFAGRDRTDIFILFPQGKVSPVQQRQMTTS 181

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
             SNVHA++++GNFDDCQNLVK MFND  F D + LSGVNSINWARIM Q+VYYFT A++
Sbjct: 182 TASNVHAVAVKGNFDDCQNLVKAMFNDQAFRDRVKLSGVNSINWARIMAQIVYYFTTAVA 241

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAPDR +SFTVPTGNFGDIFAGYVAKRMGLPI++LIIATN+NDIL+RTL++G YEMR V
Sbjct: 242 LGAPDRKISFTVPTGNFGDIFAGYVAKRMGLPIDKLIIATNENDILARTLKNGRYEMRDV 301

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             TTSPSMDIQISSNFERL+FEA+ RD A VR  M  L+QSG FTI +  L  IR EF A
Sbjct: 302 KATTSPSMDIQISSNFERLIFEANERDPAEVRAAMASLRQSGSFTIGDAALKKIRKEFRA 361

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420
           GR++  + A TI     + GYLLDPH+AIGV VA +    +APMV LATAHPAKFP AVK
Sbjct: 362 GRASEKDVAKTIRKTFDETGYLLDPHTAIGVFVATKHEKNSAPMVTLATAHPAKFPAAVK 421

Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462
           +A G++P LP WL DLM R E F +L  ELK VE ++   +R
Sbjct: 422 SASGIDPTLPTWLADLMTRAERFDILDPELKSVETFIGERTR 463


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: 624
Number of extensions: 17
Number of successful extensions: 1
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 SMc00077 SMc00077 (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.11114.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    2.2e-91  292.5   0.4    2.8e-91  292.1   0.4    1.0  1  lcl|FitnessBrowser__Smeli:SMc00077  SMc00077 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00077  SMc00077 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.1   0.4   2.8e-91   2.8e-91      14     333 ..      72     425 ..      64     431 .. 0.92

  Alignments for each domain:
  == domain 1  score: 292.1 bits;  conditional E-value: 2.8e-91
                           TIGR00260  14 dlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtg 85 
                                         +  +++   +++fr p++a  v+   n +v elfhg tlaFKD+++q +a l+ ++l +  e  t+++AtsGdtg
  lcl|FitnessBrowser__Smeli:SMc00077  72 KFREMIDEAYATFRHPAVAPLVQTgPNAFVMELFHGSTLAFKDVAMQLLARLMDYVLAERGEraTIVGATSGDTG 146
                                         566778889**********9999999*****************************876554447*********** PP

                           TIGR00260  86 aaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvN 156
                                          aa+ a+ag+   ++++L P+gk+spv + +++t  a+n++ +a+kG+FDd+q+lvk++f+d+     +kl+ vN
  lcl|FitnessBrowser__Smeli:SMc00077 147 GAAIDAFAGRDRTDIFILFPQGKVSPVqQRQMTTSTASNVHAVAVKGNFDDCQNLVKAMFNDQAfrdRVKLSGVN 221
                                         ************************************************************9877789******** PP

                           TIGR00260 157 sinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflks 231
                                         sin+ari aq++y+f  + +lg     k+ + vp gnfg+i++G+++k+++ lpi+kl ia++++ di+ r lk+
  lcl|FitnessBrowser__Smeli:SMc00077 222 SINWARIMAQIVYYFTTAVALG-APDRKISFTVPTGNFGDIFAGYVAKRMG-LPIDKLIIATNEN-DILARTLKN 293
                                         **********************.55568******************99999.************9.********* PP

                           TIGR00260 232 gdlepkedkeTlstAmdignpsnverale.larrslgnledlke.........................svsdee 280
                                         g  e +  k+T s++mdi ++sn+er+ + + +r  +++ +  +                         ++s+++
  lcl|FitnessBrowser__Smeli:SMc00077 294 GRYEMRDVKATTSPSMDIQISSNFERLIFeANERDPAEVRAAMAslrqsgsftigdaalkkirkefragRASEKD 368
                                         *76666667******************997777777777777668999*************************** PP

                           TIGR00260 281 ileaikklaeeegyllephtavavaalkklvekg...vs.atadpaKFeevvealtg 333
                                         + ++i+k   e gyll+phta++v +  k  +++   v+ ata+paKF+ +v   +g
  lcl|FitnessBrowser__Smeli:SMc00077 369 VAKTIRKTFDETGYLLDPHTAIGVFVATKHEKNSapmVTlATAHPAKFPAAVKSASG 425
                                         *************************999998888776337************98777 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.29
//
[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