Alignments for a candidate for thrC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Shewanella loihica PV-4

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 5208570 Shew_1081 threonine synthase (RefSeq)

Query= BRENDA::P00934
         (428 letters)



>FitnessBrowser__PV4:5208570
          Length = 427

 Score =  494 bits (1272), Expect = e-144
 Identities = 254/421 (60%), Positives = 313/421 (74%), Gaps = 2/421 (0%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           M+LYNLK  +++VSF QAV  GLGK++GLFFP  +P+  L  +D +L +DFV RS  +L 
Sbjct: 1   MELYNLKHPSQKVSFTQAVKLGLGKDRGLFFPVSIPK--LDNVDALLAMDFVERSKAVLG 58

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
           A++ DE+ QE+++  V  AF F  P+   +    CLELFHGPTLAFKDFG RFMAQ L  
Sbjct: 59  AWLADELGQEMVDGLVERAFNFELPLTKADDRRFCLELFHGPTLAFKDFGARFMAQCLNS 118

Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180
           +A +  +TILTATSGDTGAAVA AFYGL  V+VV+LYP+GKIS LQEK+F TLG NI TV
Sbjct: 119 LAQEDKLTILTATSGDTGAAVADAFYGLDKVQVVVLYPKGKISLLQEKMFTTLGDNIHTV 178

Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240
           A++ DFDACQ +VK AF+D +++  L LNSANSINISRLLAQICYYFEAVAQ  Q  +  
Sbjct: 179 AVESDFDACQDMVKAAFEDSDVRDGLHLNSANSINISRLLAQICYYFEAVAQFKQTNQGD 238

Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300
            V++VPSGNFG+LTAGL AK++GLPVKRF+AATN NDTVPR+L DGQWSPKAT ATLSNA
Sbjct: 239 PVIAVPSGNFGNLTAGLFAKAMGLPVKRFVAATNSNDTVPRYLADGQWSPKATVATLSNA 298

Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360
           MDV++P+NWPRVE +     W L EL    + ++ T + + EL   GY SEPHAA+A +A
Sbjct: 299 MDVAEPSNWPRVETIMEVMNWPLSELVGVGLSEQDTVEALDELYCGGYLSEPHAAIAAKA 358

Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420
           L   ++  E G+FLGTAHPAKFKE VE  L   L+LP EL    D P+LS  LPADFA L
Sbjct: 359 LSLTMSADEQGIFLGTAHPAKFKEVVEQALAIELELPPELQAVKDKPILSAELPADFARL 418

Query: 421 R 421
           +
Sbjct: 419 K 419


Lambda     K      H
   0.319    0.135    0.395 

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: 520
Number of extensions: 14
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: 428
Length of database: 427
Length adjustment: 32
Effective length of query: 396
Effective length of database: 395
Effective search space:   156420
Effective search space used:   156420
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 5208570 Shew_1081 (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.1764.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.7e-102  329.0   0.0     2e-102  328.8   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208570  Shew_1081 threonine synthase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208570  Shew_1081 threonine synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.8   0.0    2e-102    2e-102      27     331 ..      79     388 ..      50     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 328.8 bits;  conditional E-value: 2e-102
                        TIGR00260  27 rspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgnetvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                      +++ +  +    + +++elfhgPtlaFKD+g +f+a+ l+ ++++ + t+l+AtsGdtgaa+a a++g   v+vvvLy
  lcl|FitnessBrowser__PV4:5208570  79 NFELPLTKADD-RRFCLELFHGPTLAFKDFGARFMAQCLNSLAQEDKLTILTATSGDTGAAVADAFYGLDKVQVVVLY 155
                                      55444444444.779*************************************************************** PP

                        TIGR00260 105 PkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgk 179
                                      Pkgkis+++ek++t+l  n++++a++ dFD++qd+vk++fed+     l lns+Nsin++r++aq++y+fe+v+q ++
  lcl|FitnessBrowser__PV4:5208570 156 PKGKISLLQEKMFTTLGDNIHTVAVESDFDACQDMVKAAFEDSDvrdGLHLNSANSINISRLLAQICYYFEAVAQFKQ 233
                                      ******99*********************************7777789****************************** PP

                        TIGR00260 180 espdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnver 257
                                       ++   v++vpsgnfg++++G ++k ++ lp  k+++aa++++d+v+r+l +g+++pk++++Tls+Amd+ +psn++r
  lcl|FitnessBrowser__PV4:5208570 234 TNQGDPVIAVPSGNFGNLTAGLFAKAMG-LP-VKRFVAATNSNDTVPRYLADGQWSPKATVATLSNAMDVAEPSNWPR 309
                                      999999***************9999998.**.88899988889*********************************** PP

                        TIGR00260 258 alelarrslgnledl.kesvsdeeileaikklaeeegyllephtavavaalkklvekg.vs...atadpaKFeevve. 329
                                      ++ +++  ++ l +l + ++s+++++ea  +l+   gyl eph+a+a +al  ++ ++ ++   +ta+paKF+evve 
  lcl|FitnessBrowser__PV4:5208570 310 VETIMEVMNWPLSELvGVGLSEQDTVEALDELYC-GGYLSEPHAAIAAKALSLTMSADeQGiflGTAHPAKFKEVVEq 386
                                      **********9988626699***********996.7*******************999766889************95 PP

                        TIGR00260 330 al 331
                                      al
  lcl|FitnessBrowser__PV4:5208570 387 AL 388
                                      54 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (427 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: 10.60
//
[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