Alignments for a candidate for thrC in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Pseudomonas fluorescens FW300-N2C3

Align Threonine synthase; TS; EC 4.2.3.1 (characterized)
to candidate AO356_06370 AO356_06370 threonine synthase

Query= SwissProt::P16120
         (514 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_06370
          Length = 469

 Score =  347 bits (889), Expect = e-100
 Identities = 204/485 (42%), Positives = 290/485 (59%), 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  + + PL Q + G   N  ++ELFHGPT AFKD A
Sbjct: 61  PFVTGS-IPDADFKKILEETYGVFSHNAIAPLRQ-LNG---NEWVMELFHGPTLAFKDFA 115

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

Query: 188 RISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFNSKHNVGAVNSINWARI 247
           R+S +Q  QMTT+  +N+  +++ G FD+CQ++VKA F D+ F     + AVNSINWARI
Sbjct: 168 RVSEVQRRQMTTIFGDNIHNIAIEGNFDDCQEMVKASFADQSFLKGTRLVAVNSINWARI 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
              +  G F V+      A K F S  V +E+T ETI +++  S      +LDPHTA+GV
Sbjct: 336 DSFRQGGGFSVEPERWTEARKLFDSLAVDDEQTCETIAEVFAQSGE----LLDPHTAIGV 391

Query: 428 CATERLIAKDNDKSIQYISLSTAHPAKFADAVNNA-------LSGFSNYSFEKD----VL 476
            A            +  + L TAHP KF +AV  A       L    +  FE+D    VL
Sbjct: 392 RAAREC---RRSLDLPMVILGTAHPVKFPEAVEKAGVGKALELPAHLSDLFERDERCTVL 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: 594
Number of extensions: 28
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 AO356_06370 AO356_06370 (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.30496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    1.1e-84  270.5   0.0    1.3e-84  270.2   0.0    1.1  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370  AO356_06370 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370  AO356_06370 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.2   0.0   1.3e-84   1.3e-84      10     337 ..      67     430 ..      58     433 .. 0.92

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 1.3e-84
                                       TIGR00260  10 vtekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkale 70 
                                                     ++++d +++ e  + +f  +++a  +++ + n +v elfhgPtlaFKD++lq ++ ll ++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370  67 IPDADFKKILEETYGVFSHNAIAplRQLNG-NEWVMELFHGPTLAFKDFALQLLGRLLDYVLQ 128
                                                     4588999999999****9999988899999.99****************************99 PP

                                       TIGR00260  71 lgne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaik 130
                                                     +  e  ++++AtsGdtg+aa+e+ +  +nv++++L P+ ++s v   +++t    n++ +ai+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370 129 KRGErvVIVGATSGDTGSAAIEGCKHCENVDIFILHPHNRVSEVqRRQMTTIFGDNIHNIAIE 191
                                                     887778999***********************************99***************** PP

                                       TIGR00260 131 GdFDdaqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp 190
                                                     G+FDd+q++vk+ f d+     + l++vNsin+ari aq++y+f ++ qlg+ +   v ++vp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370 192 GNFDDCQEMVKASFADQSflkGTRLVAVNSINWARIMAQIVYYFHAALQLGGPA-RSVSFSVP 253
                                                     **************977779899****************************655.57****** PP

                                       TIGR00260 191 sgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignps 253
                                                      gnfg+i++G+l+ +++ lpi+ l +a++ + di++rf+ + + ++ +  +Tls++mdi  +s
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370 254 TGNFGDIFAGYLARNMG-LPINQLIVATNRN-DILHRFMSGNQYVKETLHATLSPSMDIMVSS 314
                                                     **********9999999.******9999998.******877777777777************* PP

                                       TIGR00260 254 nverale.larrslgnledlke.........................svsdeeileaikklae 290
                                                     n+er+l+ l  r+++ +  l                           +v de++ e+i ++ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370 315 NFERLLFdLHGRNGAAIAGLMDsfrqgggfsveperwtearklfdslAVDDEQTCETIAEVFA 377
                                                     ******99999999999999779999************************************* PP

                                       TIGR00260 291 eegyllephtavavaalkklvekg...vs..atadpaKFeevve.altgnklk 337
                                                     + g ll+phta++v+a ++   +    +   +ta+p KF+e+ve a  g+ l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06370 378 QSGELLDPHTAIGVRAARECRRSLdlpMVilGTAHPVKFPEAVEkAGVGKALE 430
                                                     ****************998887666662257************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.61
//
[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:

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, 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

GapMind for Amino acid biosynthesis