GapMind for Amino acid biosynthesis

 

Aligments for a candidate for thrC in Pseudomonas fluorescens FW300-N1B4

Align Threonine synthase; TS; EC 4.2.3.1 (characterized)
to candidate Pf1N1B4_3014 Threonine synthase (EC 4.2.3.1)

Query= SwissProt::P16120
         (514 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014 Threonine synthase
           (EC 4.2.3.1)
          Length = 469

 Score =  350 bits (899), Expect = e-101
 Identities = 208/485 (42%), Positives = 291/485 (60%), Gaps = 45/485 (9%)

Query: 8   YRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAIMR 67
           Y STR  +P  ++FE+ ++ GLATDGGL++P  +P+  Q  + + W+ L + +LAF +MR
Sbjct: 3   YISTRGQAP-ALNFEDVLLAGLATDGGLYVPENLPRFTQEEIAS-WAGLPYHELAFRVMR 60

Query: 68  LYIAQEEIPDADLKDLIKRSYSTFRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDVA 127
            ++    IPDAD K +++ +Y  F  + V PL Q + G   N  +LELFHGPT AFKD A
Sbjct: 61  PFVTGS-IPDADFKKILEETYGVFSHNAVAPLRQ-LNG---NEWVLELFHGPTLAFKDFA 115

Query: 128 LQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPTG 187
           LQ +G L +Y L++       GE+  + +VGATSGDTGSAAI G +  ++V +FIL+P  
Sbjct: 116 LQLLGRLLDYVLEK------RGER--VVIVGATSGDTGSAAIEGCKHCENVDIFILHPHN 167

Query: 188 RISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFNSKHNVGAVNSINWARI 247
           R+S +Q  QMTT+  EN+  +++ G FD+CQ++VKA F D+ F     + AVNSINWARI
Sbjct: 168 RVSEVQRRQMTTIFGENIHNIAIEGNFDDCQEMVKASFADQSFLKGTRLVAVNSINWARI 227

Query: 248 LAQMTYYFYSFFQATNGKDSKKVKFVVPSGNFGDILAGYFAKKMGLPIEKLAIATNENDI 307
           +AQ+ YYF++  Q   G  ++ V F VP+GNFGDI AGY A+ MGLPI +L +ATN NDI
Sbjct: 228 MAQIVYYFHAALQL--GGPARSVSFSVPTGNFGDIFAGYLARNMGLPINQLIVATNRNDI 285

Query: 308 LDRFLKSGLYERSDKVAATLSPAMDILISSNFERLLWYLAREYLANGDDLKAGEIVNNWF 367
           L RF+    Y + + + ATLSP+MDI++SSNFERLL+ L           + G  +    
Sbjct: 286 LHRFMSGNQYVK-ETLHATLSPSMDIMVSSNFERLLFDLHG---------RNGAAIAGLM 335

Query: 368 QELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYILDPHTAVGV 427
              K  G F V++     A K F S  V + +T ETI +++E +      +LDPHTA+GV
Sbjct: 336 DTFKQGGGFSVEEERWTEARKLFDSLAVDDAQTCETIAEVFEQTGE----LLDPHTAIGV 391

Query: 428 CATERLIAKDNDKSIQYISLSTAHPAKFADAVNNA-------LSGFSNYSFEKD----VL 476
            A            I  + L TAHP KF DAV  A       L    +  FE+D    VL
Sbjct: 392 KAAREC---RRSLDIPMVILGTAHPVKFPDAVEKAGVGKALELPAHLSDLFERDERCTVL 448

Query: 477 PEELK 481
           P +LK
Sbjct: 449 PNDLK 453


Lambda     K      H
   0.316    0.133    0.374 

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: 607
Number of extensions: 31
Number of successful extensions: 10
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: 514
Length of database: 469
Length adjustment: 34
Effective length of query: 480
Effective length of database: 435
Effective search space:   208800
Effective search space used:   208800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Pf1N1B4_3014 (Threonine synthase (EC 4.2.3.1))
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.6278.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    2.4e-85  272.6   0.0      3e-85  272.3   0.0    1.1  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014  Threonine synthase (EC 4.2.3.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014  Threonine synthase (EC 4.2.3.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.3   0.0     3e-85     3e-85      10     337 ..      67     430 ..      58     433 .. 0.92

  Alignments for each domain:
  == domain 1  score: 272.3 bits;  conditional E-value: 3e-85
                                      TIGR00260  10 vtekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalel 71 
                                                    ++++d +++ e  + +f  +++a  +++ + n +v+elfhgPtlaFKD++lq ++ ll ++le+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014  67 IPDADFKKILEETYGVFSHNAVAplRQLNG-NEWVLELFHGPTLAFKDFALQLLGRLLDYVLEK 129
                                                    4588999999999****9999988899999.99*****************************99 PP

                                      TIGR00260  72 gne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGd 132
                                                      e  ++++AtsGdtg+aa+e+ +  +nv++++L P+ ++s v   +++t   en++ +ai+G+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014 130 RGErvVIVGATSGDTGSAAIEGCKHCENVDIFILHPHNRVSEVqRRQMTTIFGENIHNIAIEGN 193
                                                    8777899************************************99******************* PP

                                      TIGR00260 133 FDdaqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgn 193
                                                    FDd+q++vk+ f d+     + l++vNsin+ari aq++y+f ++ qlg+ +   v ++vp gn
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014 194 FDDCQEMVKASFADQSflkGTRLVAVNSINWARIMAQIVYYFHAALQLGGPA-RSVSFSVPTGN 256
                                                    ************977779899****************************655.57********* PP

                                      TIGR00260 194 fgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnver 257
                                                    fg+i++G+l+ +++ lpi+ l +a++ + di++rf+ + + ++ +  +Tls++mdi  +sn+er
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014 257 FGDIFAGYLARNMG-LPINQLIVATNRN-DILHRFMSGNQYVKETLHATLSPSMDIMVSSNFER 318
                                                    *******9999999.******9999998.******877777777777***************** PP

                                      TIGR00260 258 ale.larrslgnledlke.........................svsdeeileaikklaeeegyl 295
                                                    +l+ l  r+++ +  l                           +v d+++ e+i ++ e+ g l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014 319 LLFdLHGRNGAAIAGLMDtfkqgggfsveeerwtearklfdslAVDDAQTCETIAEVFEQTGEL 382
                                                    **99999999999988669999****************************************** PP

                                      TIGR00260 296 lephtavavaalkklvekg...vs..atadpaKFeevve.altgnklk 337
                                                    l+phta++v+a ++   +    +   +ta+p KF+++ve a  g+ l+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3014 383 LDPHTAIGVKAARECRRSLdipMVilGTAHPVKFPDAVEkAGVGKALE 430
                                                    ***********998887666652257************9777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (469 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: 8.35
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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, or view the source code, or see 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