Alignments for a candidate for thrC in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Phaeobacter inhibens BS107

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate GFF617 PGA1_c06310 threonine synthase ThrC

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__Phaeo:GFF617
          Length = 462

 Score =  518 bits (1335), Expect = e-151
 Identities = 264/460 (57%), Positives = 333/460 (72%), Gaps = 1/460 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           MKY+STRG+AP L F DA+L GLARDGGLY+P E P  + ++I AL G SY EVA  V+ 
Sbjct: 1   MKYISTRGQAPELTFEDAMLTGLARDGGLYVPAEIPTMSKDEIAALAGLSYEEVAFRVMR 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF G      +F  ++  AY  F H A  PLVQ   N F+LELFHGPTLAFKD AMQL+ 
Sbjct: 61  PFLGDCFTDEEFRGIIARAYDGFGHAARAPLVQLAPNHFLLELFHGPTLAFKDFAMQLIG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           ++ +  L +RGE  TIVGATSGDTG AAI+AFGG D  ++FIL+P+GRVS VQ+RQMT+ 
Sbjct: 121 QLFETALKRRGESVTIVGATSGDTGSAAIQAFGGLDAVNVFILYPHGRVSEVQRRQMTTP 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
             +NVHAL+++G+FDDCQ  +K MFND +F D + L+GVNSIN+AR++ QVVYYFT+A+S
Sbjct: 181 TDANVHALAVDGDFDDCQAALKDMFNDFDFRDEVRLAGVNSINFARVLAQVVYYFTSAVS 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAP+R VSFTVPTGNFGDIFAG++AK+MGLPI+QL++ATN NDIL R L    Y     
Sbjct: 241 LGAPERKVSFTVPTGNFGDIFAGFIAKQMGLPIDQLVVATNQNDILHRCLSGQGYHKGET 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             + SPSMDIQ+SSNFER LF A G+D AAV  LM  LK SGGF +S+  + A++  + +
Sbjct: 301 IPSISPSMDIQVSSNFERALFYACGQDGAAVAQLMDELK-SGGFEVSQGAMQALQEHYVS 359

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420
           GR + +ET+ATI+S  +  G LL PHSAIGVKVA E+     PMV LATAHPAKFP AV+
Sbjct: 360 GRCSEEETSATIKSERAASGELLCPHSAIGVKVANEQRDAAVPMVTLATAHPAKFPAAVE 419

Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460
            A G+ P LP  + DL  R E  T + N+L  +E ++R H
Sbjct: 420 EASGIHPPLPPRMADLYDRSERVTRIANDLTTLETHIRKH 459


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: 570
Number of extensions: 19
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: 462
Length adjustment: 33
Effective length of query: 430
Effective length of database: 429
Effective search space:   184470
Effective search space used:   184470
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 GFF617 PGA1_c06310 (threonine synthase ThrC)
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.12229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.6e-83  265.9   0.0    3.4e-83  265.5   0.0    1.1  1  lcl|FitnessBrowser__Phaeo:GFF617  PGA1_c06310 threonine synthase T


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF617  PGA1_c06310 threonine synthase ThrC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.5   0.0   3.4e-83   3.4e-83      37     334 ..      94     424 ..      63     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 265.5 bits;  conditional E-value: 3.4e-83
                         TIGR00260  37 a.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkis 110
                                       +  n +++elfhgPtlaFKD+++q +++l++ al++  e  t+++AtsGdtg+aa++a+ g   v+v++LyP+g++s
  lcl|FitnessBrowser__Phaeo:GFF617  94 LaPNHFLLELFHGPTLAFKDFAMQLIGQLFETALKRRGEsvTIVGATSGDTGSAAIQAFGGLDAVNVFILYPHGRVS 170
                                       345889*************************9999877778************************************ PP

                         TIGR00260 111 pv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgkespd 183
                                        v   +++t  + n++ la++GdFDd+q+++k++f+d     ++ l  vNsin+ar++aq++y+f  +  lg   + 
  lcl|FitnessBrowser__Phaeo:GFF617 171 EVqRRQMTTPTDANVHALAVDGDFDDCQAALKDMFNDFDfrdEVRLAGVNSINFARVLAQVVYYFTSAVSLG-APER 246
                                       **99*******************************94334679*****************************.7778 PP

                         TIGR00260 184 kvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale 260
                                       kv + vp gnfg+i++Gf +k+++ lpi+ l +a++++ di++r l ++   + e+   +s++mdi  +sn+eral+
  lcl|FitnessBrowser__Phaeo:GFF617 247 KVSFTVPTGNFGDIFAGFIAKQMG-LPIDQLVVATNQN-DILHRCLSGQGYHKGETIPSISPSMDIQVSSNFERALF 321
                                       9******************99999.************9.******999989999999*******************9 PP

                         TIGR00260 261 .larrslgnledlke........................svsdeeileaikklaeeegyllephtavavaalkklve 312
                                        +  + ++ + +l                          ++s+ee++ +ik   +  g ll ph+a++v++ +++ +
  lcl|FitnessBrowser__Phaeo:GFF617 322 yACGQDGAAVAQLMDelksggfevsqgamqalqehyvsgRCSEEETSATIKSERAASGELLCPHSAIGVKVANEQRD 398
                                       7666666665555446777********************************************************** PP

                         TIGR00260 313 kg...vs.atadpaKFeevvealtgn 334
                                       +    v+ ata+paKF+ +ve  +g 
  lcl|FitnessBrowser__Phaeo:GFF617 399 AAvpmVTlATAHPAKFPAAVEEASGI 424
                                       99876337************987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (462 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: 12.36
//
[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