Alignments for a candidate for thrC in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Dinoroseobacter shibae DFL-12

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 3607737 Dshi_1146 threonine synthase (RefSeq)

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__Dino:3607737
          Length = 463

 Score =  517 bits (1332), Expect = e-151
 Identities = 263/458 (57%), Positives = 326/458 (71%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+Y+STRG+AP + F +A+LAGLA DGGLY+P+  P  T  +IRA+ G  Y E+A  V+ 
Sbjct: 1   MRYISTRGQAPAMAFHEAMLAGLASDGGLYVPETVPTLTEAEIRAMAGLPYEEIAFRVMM 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF G      +F   +  AYG F HDA  PL Q   N F+LELFHGPTLAFKD AMQL+ 
Sbjct: 61  PFLGNSFTEEEFRTDIATAYGGFGHDARAPLKQLGPNHFLLELFHGPTLAFKDFAMQLIG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           ++    L +RG R TIVGATSGDTG AAIEAF G  + D+FIL+P+GRVS VQ+RQMT+ 
Sbjct: 121 QLFQRELTRRGSRVTIVGATSGDTGSAAIEAFRGIASVDVFILYPHGRVSEVQRRQMTTP 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
              NVHAL++ G+FDDCQ  +K MFND  F D + L+GVNSINWAR++ QVVYYF+AA S
Sbjct: 181 TEDNVHALALHGHFDDCQARLKDMFNDHGFRDGVRLAGVNSINWARVLAQVVYYFSAATS 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAPDR +SFTVPTGNFGDIFAGY+A+RMGLPI+ L+IATN NDIL R L +GAYE   V
Sbjct: 241 LGAPDRKISFTVPTGNFGDIFAGYIARRMGLPIDTLVIATNQNDILHRCLTTGAYETDAV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             + SPSMDIQ+SSNFERLLF+ + RD AAV  LM  LK  GGFT+S+  L+ +R  F++
Sbjct: 301 IPSISPSMDIQVSSNFERLLFDVYDRDGAAVAQLMDELKTKGGFTLSQGALTRLREGFAS 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420
           GR++ DET+ATI         LL PHSA+GV VA +      PMV LATAHPAKFP AV+
Sbjct: 361 GRASEDETSATITRARDTMNELLCPHSAVGVHVAEQHIEPGVPMVTLATAHPAKFPAAVE 420

Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVR 458
           AA GV P LP  +  L +R E  T + N+L  ++  +R
Sbjct: 421 AATGVHPPLPPRMETLYERPERLTEVPNDLGALQTLIR 458


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: 585
Number of extensions: 16
Number of successful extensions: 1
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: 463
Length adjustment: 33
Effective length of query: 430
Effective length of database: 430
Effective search space:   184900
Effective search space used:   184900
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 3607737 Dshi_1146 (threonine synthase (RefSeq))
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.15136.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    4.2e-82  262.0   0.0    5.4e-82  261.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607737  Dshi_1146 threonine synthase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607737  Dshi_1146 threonine synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.6   0.0   5.4e-82   5.4e-82      30     334 ..      89     425 ..      69     430 .. 0.92

  Alignments for each domain:
  == domain 1  score: 261.6 bits;  conditional E-value: 5.4e-82
                         TIGR00260  30 klaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                       ++ +++g  n +++elfhgPtlaFKD+++q +++l+++ l +     t+++AtsGdtg+aa+ea++g a v+v++Ly
  lcl|FitnessBrowser__Dino:3607737  89 APLKQLGP-NHFLLELFHGPTLAFKDFAMQLIGQLFQRELTRRGSrvTIVGATSGDTGSAAIEAFRGIASVDVFILY 164
                                       55678888.99*************************98665544447****************************** PP

                         TIGR00260 105 Pkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqktyafeiveql 177
                                       P+g++s v   +++t    n++ la +G FDd+q+ +k++f+d+     + l  vNsin+ar++aq++y+f+++  l
  lcl|FitnessBrowser__Dino:3607737 165 PHGRVSEVqRRQMTTPTEDNVHALALHGHFDDCQARLKDMFNDHGfrdGVRLAGVNSINWARVLAQVVYYFSAATSL 241
                                       ********99*******************************96555779**************************** PP

                         TIGR00260 178 gkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsn 254
                                       g     k+ + vp gnfg+i++G+ + +++ lpi+ l ia++++ di++r l +g  e+ +    +s++mdi  +sn
  lcl|FitnessBrowser__Dino:3607737 242 G-APDRKISFTVPTGNFGDIFAGYIARRMG-LPIDTLVIATNQN-DILHRCLTTGAYETDAVIPSISPSMDIQVSSN 315
                                       *.55568****************9999999.************9.**********88888888************** PP

                         TIGR00260 255 verale.larrslgnledlke.........................svsdeeileaikklaeeegyllephtavava 305
                                       +er+l+ +  r ++ + +l                           ++s++e++ +i ++  + + ll ph+av+v 
  lcl|FitnessBrowser__Dino:3607737 316 FERLLFdVYDRDGAAVAQLMDelktkggftlsqgaltrlregfasgRASEDETSATITRARDTMNELLCPHSAVGVH 392
                                       ******7777888777777557888**************************************************** PP

                         TIGR00260 306 alkklvekg...vs.atadpaKFeevvealtgn 334
                                       + ++ +e g   v+ ata+paKF+ +vea tg 
  lcl|FitnessBrowser__Dino:3607737 393 VAEQHIEPGvpmVTlATAHPAKFPAAVEAATGV 425
                                       *********876337*************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (463 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: 10.03
//
[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