Alignments for a candidate for thrC in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Shewanella oneidensis MR-1

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 202520 SO3413 threonine synthase (NCBI ptt file)

Query= BRENDA::P00934
         (428 letters)



>FitnessBrowser__MR1:202520
          Length = 427

 Score =  478 bits (1230), Expect = e-139
 Identities = 248/421 (58%), Positives = 304/421 (72%), Gaps = 2/421 (0%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           M+LYNLK  ++ VSF +AV  GLGK++GLFFP  +P   L +I+ +L + FV RS K+L 
Sbjct: 1   MELYNLKHPSQTVSFKEAVQLGLGKDRGLFFPTQIPV--LHDIEALLAMPFVERSKKVLG 58

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
           A++  E+ Q+++++ V  AF F  P+  V+    CLELFHGPTLAFKDFG RFMAQ +  
Sbjct: 59  AWLASELGQDMVDQLVERAFNFDLPLVAVDEQRACLELFHGPTLAFKDFGARFMAQCINV 118

Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180
            A D  +TILTATSGDTGAAVA AFYGL  V VV+LYP+GKIS LQEK+F TLG NI TV
Sbjct: 119 FAQDSRLTILTATSGDTGAAVADAFYGLEKVNVVVLYPKGKISELQEKMFTTLGKNIHTV 178

Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240
           A+  DFDACQ LVKQAF+D +++  L LNSANSINISRLLAQICYYFEAVAQ  Q     
Sbjct: 179 AVASDFDACQHLVKQAFEDSDVRDGLHLNSANSINISRLLAQICYYFEAVAQSKQRHEAD 238

Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300
            V++VPSGNFG+LTAGL AK++GLPVKRFIAATN NDTVPR+L  G W P  TQAT+SNA
Sbjct: 239 PVIAVPSGNFGNLTAGLFAKAMGLPVKRFIAATNANDTVPRYLDSGHWQPNPTQATMSNA 298

Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360
           MDVS+P+NWPRVE +  +  W L +L    + +  T + + +L   GY SEPHAA+A +A
Sbjct: 299 MDVSEPSNWPRVEAICEKLGWPLADLVGICLSEAQTSEALVDLYAKGYVSEPHAAIAAKA 358

Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420
           L   L P E G+FLGTAHPAKFK+ V+  L   L LP EL   A  P+LS  L ADFA L
Sbjct: 359 LTLNLVPDEVGIFLGTAHPAKFKDVVDRELALNLPLPPELKAVAHKPILSAELAADFAQL 418

Query: 421 R 421
           +
Sbjct: 419 K 419


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: 509
Number of extensions: 16
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: 428
Length of database: 427
Length adjustment: 32
Effective length of query: 396
Effective length of database: 395
Effective search space:   156420
Effective search space used:   156420
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 202520 SO3413 (threonine synthase (NCBI ptt file))
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.28079.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.3e-101  323.5   0.0     1e-100  323.2   0.0    1.0  1  lcl|FitnessBrowser__MR1:202520  SO3413 threonine synthase (NCBI 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202520  SO3413 threonine synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.2   0.0    1e-100    1e-100      12     329 ..      64     385 ..      50     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: 323.2 bits;  conditional E-value: 1e-100
                       TIGR00260  12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgnetvlcAtsGdtgaaaae 90 
                                     e  +  +++ + ++f+++ +   v + +  ++elfhgPtlaFKD+g +f+a+ ++ ++++ + t+l+AtsGdtgaa+a 
  lcl|FitnessBrowser__MR1:202520  64 ELGQDMVDQLVERAFNFDLPLVAVDE-QRACLELFHGPTLAFKDFGARFMAQCINVFAQDSRLTILTATSGDTGAAVAD 141
                                     45555666777788888888888887.6689************************************************ PP

                       TIGR00260  91 alagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaq 166
                                     a++g + v+vvvLyPkgkis ++ek++t+l +n++++a+  dFD++q+lvk++fed+     l lns+Nsin++r++aq
  lcl|FitnessBrowser__MR1:202520 142 AFYGLEKVNVVVLYPKGKISELQEKMFTTLGKNIHTVAVASDFDACQHLVKQAFEDSDvrdGLHLNSANSINISRLLAQ 220
                                     *******************************************************7777789***************** PP

                       TIGR00260 167 ktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlst 245
                                     ++y+fe+v+q +++++   v++vpsgnfg++++G ++k ++ lp  k++iaa++a+d+v+r+l sg+++p  +++T+s+
  lcl|FitnessBrowser__MR1:202520 221 ICYYFEAVAQSKQRHEADPVIAVPSGNFGNLTAGLFAKAMG-LP-VKRFIAATNANDTVPRYLDSGHWQPNPTQATMSN 297
                                     **********************************9999998.**.99******************************** PP

                       TIGR00260 246 Amdignpsnveralelarrslgnledlkesv.sdeeileaikklaeeegyllephtavavaalkklvekg.vs...ata 319
                                     Amd+++psn++r++++ ++ ++ l dl   + s+++++ea   l++ +gy+ eph+a+a +al   +  + v+   +ta
  lcl|FitnessBrowser__MR1:202520 298 AMDVSEPSNWPRVEAICEKLGWPLADLVGIClSEAQTSEALVDLYA-KGYVSEPHAAIAAKALTLNLVPDeVGiflGTA 375
                                     **********************999986655155666667666665.8**************97666666555778*** PP

                       TIGR00260 320 dpaKFeevve 329
                                     +paKF++vv 
  lcl|FitnessBrowser__MR1:202520 376 HPAKFKDVVD 385
                                     ********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (427 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 14.17
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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