Alignments for a candidate for thrC in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Methylocella silvestris BL2

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012590290.1 MSIL_RS06420 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000021745.1:WP_012590290.1
          Length = 473

 Score =  545 bits (1403), Expect = e-159
 Identities = 277/461 (60%), Positives = 341/461 (73%), Gaps = 3/461 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           MKYVSTRGEA  L F+  LLAGLA DGGLYLP+ YP+  AE+I +  GKSY +V  AV++
Sbjct: 1   MKYVSTRGEAAPLSFTQTLLAGLAPDGGLYLPESYPRLDAERIASFSGKSYTDVTEAVIS 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF GGEI  A    M+ +AY  FRH AV PLVQ D N F LELFHGPTLAFKD+AMQLLA
Sbjct: 61  PFIGGEIVPAALRAMIDDAYAGFRHPAVAPLVQLDDNLFTLELFHGPTLAFKDLAMQLLA 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R++D+ L  RG+RAT+VGATSGDTG AAIEAF G    ++FIL+P+ RVS VQ+RQMT++
Sbjct: 121 RLVDHALKARGQRATVVGATSGDTGAAAIEAFSGLSQVEVFILYPHQRVSEVQRRQMTTT 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
           G  NVHA+++EG+FDD Q+ VK +FN+    ++L+L GVNSINWARI+ Q VYYFTAA++
Sbjct: 181 GAPNVHAIAVEGSFDDAQSAVKALFNNRPLRESLNLCGVNSINWARILAQTVYYFTAAVA 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAP R VSF  PTGNFGDIFAG++AKRMGLPI++L+IA N NDIL R LESGAY +  V
Sbjct: 241 LGAPHRPVSFVTPTGNFGDIFAGWIAKRMGLPIDRLVIAANSNDILPRALESGAYAVGEV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             T SPSMDIQ+SSNFERLLFEA GRD AAVR  M  L QS GFTI   PL AIR++F A
Sbjct: 301 HATQSPSMDIQVSSNFERLLFEAQGRDGAAVRAWMAQLSQSRGFTIDPAPLKAIRADFDA 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKAS---GTAPMVVLATAHPAKFPD 417
              +  ET A I  +  + GYL DPH+A+G+  AR + +      P+VVL TAH AKFPD
Sbjct: 361 FSVSEPETTAEIARLWRESGYLADPHTAVGLGAARREIATRGAATPLVVLGTAHAAKFPD 420

Query: 418 AVKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVR 458
           A++AA GV P LP  L  L++R E F+++ N+   VE ++R
Sbjct: 421 AIEAATGVRPALPPHLHGLLERAEQFSIIPNDQGAVERFIR 461


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: 599
Number of extensions: 25
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: 473
Length adjustment: 33
Effective length of query: 430
Effective length of database: 440
Effective search space:   189200
Effective search space used:   189200
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_012590290.1 MSIL_RS06420 (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.29097.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-86  277.1   0.0    1.3e-86  276.8   0.0    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012590290.1  MSIL_RS06420 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012590290.1  MSIL_RS06420 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.8   0.0   1.3e-86   1.3e-86      15     334 ..      72     428 ..      63     433 .. 0.91

  Alignments for each domain:
  == domain 1  score: 276.8 bits;  conditional E-value: 1.3e-86
                                 TIGR00260  15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 
                                               l +++   ++ fr p++a  v++  nl+ +elfhgPtlaFKD+++q +a l+ +al++  +  tv++At
  lcl|NCBI__GCF_000021745.1:WP_012590290.1  72 LRAMIDDAYAGFRHPAVAPLVQLdDNLFTLELFHGPTLAFKDLAMQLLARLVDHALKARGQraTVVGAT 140
                                               66777888999*******9999999*****************************988655456****** PP

                                 TIGR00260  81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke 148
                                               sGdtgaaa+ea++g + v+v++LyP+ ++s v   +++t+ a n++ +a++G FDdaq +vk++f++++
  lcl|NCBI__GCF_000021745.1:WP_012590290.1 141 SGDTGAAAIEAFSGLSQVEVFILYPHQRVSEVqRRQMTTTGAPNVHAIAVEGSFDDAQSAVKALFNNRP 209
                                               ********************************99********************************666 PP

                                 TIGR00260 149 ...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiekl 214
                                                   l+l  vNsin+ari+aq +y+f ++ +lg      v ++ p gnfg+i++G+ +k+++ lpi+ l
  lcl|NCBI__GCF_000021745.1:WP_012590290.1 210 lreSLNLCGVNSINWARILAQTVYYFTAAVALG-APHRPVSFVTPTGNFGDIFAGWIAKRMG-LPIDRL 276
                                               666******************************.66667999999**********9999999.****** PP

                                 TIGR00260 215 aiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke........ 274
                                                iaa+++ di++r l+sg     e  +T s++mdi  +sn+er+l+ +  r ++ +    +        
  lcl|NCBI__GCF_000021745.1:WP_012590290.1 277 VIAANSN-DILPRALESGAYAVGEVHATQSPSMDIQVSSNFERLLFeAQGRDGAAVR---Awmaqlsqs 341
                                               ******9.**********88888888******************9744444444444...34459999* PP

                                 TIGR00260 275 ....................svsdeeileaikklaeeegyllephtavavaalkklvekg..vs..... 316
                                                                   svs+ e++ +i +l +e gyl++phtav++ a ++ ++     +     
  lcl|NCBI__GCF_000021745.1:WP_012590290.1 342 rgftidpaplkairadfdafSVSEPETTAEIARLWRESGYLADPHTAVGLGAARREIATRgaATplvvl 410
                                               ********************************************************9987761145667 PP

                                 TIGR00260 317 atadpaKFeevvealtgn 334
                                               +ta+ aKF++++ea tg 
  lcl|NCBI__GCF_000021745.1:WP_012590290.1 411 GTAHAAKFPDAIEAATGV 428
                                               *************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (473 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: 10.22
//
[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