Alignments for a candidate for thrC in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Ammonifex degensii KC4

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_015738594.1 ADEG_RS02880 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000024605.1:WP_015738594.1
          Length = 500

 Score =  288 bits (736), Expect = 4e-82
 Identities = 175/440 (39%), Positives = 254/440 (57%), Gaps = 20/440 (4%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M Y STRG+AP +  ++ +L GLA DGGLY+P+ +P+     I  L   SY E A+ +++
Sbjct: 1   MLYESTRGQAPPVKAAETILQGLAPDGGLYVPEFFPRLRFSSIEELSRHSYPEQAVRLIS 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDA--VCPLVQTDANEFVLELFHGPTLAFKDVAMQL 118
            F     PA +    V  AY   + D   + PL     +  +LEL+HGPT AFKD+A+ L
Sbjct: 61  LFLTDFSPA-EVSSAVLAAYNPLKFDTEEIVPLKVLAPDVGILELWHGPTHAFKDLALTL 119

Query: 119 LARMMDYVLAQRG--ERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQ 176
           L  +M     + G  +   I+ ATSGDTG AA+E+F     T I + FP+  VS +Q+RQ
Sbjct: 120 LPHLMTRATQKLGLEKEIVILVATSGDTGKAALESFRDVPKTRIIVFFPSEGVSEIQKRQ 179

Query: 177 MTSSGFSNVHALSIEGNFDDCQNLVKGMFNDLEF-----CDALSLSGVNSINWARIMPQV 231
           M +    N   +++EGNFDD Q+ VK +F D E         ++ S  NSINW R++PQV
Sbjct: 180 MITQEGENTFVVAVEGNFDDAQSGVKQLFGDPELRRKMESAGMTFSSANSINWGRLLPQV 239

Query: 232 VYYFTAAL-----SLGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDIL 286
           VYYF+A        L      ++F VPTGNFG+I AG++A+ MGLP+ +LI+A N N++L
Sbjct: 240 VYYFSAYARLLRDKLIRHGEEINFVVPTGNFGNILAGFLAREMGLPVRRLILAANANNVL 299

Query: 287 SRTLESGAYE-MRGVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFT 345
           +  + +G Y+  R   +T SPSMDI ISSN ERLL+    R+A  VR  M  L ++G + 
Sbjct: 300 TDFINTGIYDRRRPFHRTISPSMDILISSNLERLLYLVTDRNAEKVRQWMTSLARTGVYQ 359

Query: 346 ISEKPLSAIRSEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKV---AREKASGTA 402
           I +     I+  F +  ++ DET A I+   ++ GYLLDPH+ +   V    RE+   + 
Sbjct: 360 IDQATHERIKQVFWSSWASDDETLAAIKDAYTRYGYLLDPHTGVAWHVFNRYREETGDST 419

Query: 403 PMVVLATAHPAKFP-DAVKA 421
             V+L+TA P KF  D ++A
Sbjct: 420 KTVILSTASPFKFARDVIRA 439


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: 510
Number of extensions: 36
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 463
Length of database: 500
Length adjustment: 34
Effective length of query: 429
Effective length of database: 466
Effective search space:   199914
Effective search space used:   199914
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 WP_015738594.1 ADEG_RS02880 (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.11801.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.9e-77  246.1   0.0    3.7e-77  245.7   0.0    1.1  1  lcl|NCBI__GCF_000024605.1:WP_015738594.1  ADEG_RS02880 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738594.1  ADEG_RS02880 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.7   0.0   3.7e-77   3.7e-77      29     336 ..      87     445 ..      64     449 .. 0.87

  Alignments for each domain:
  == domain 1  score: 245.7 bits;  conditional E-value: 3.7e-77
                                 TIGR00260  29 pkla.eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalel.gne...tvlcAtsGdtgaaaaeal 92 
                                               +++   +v a ++ ++el hgPt aFKD++l  +  l+t+a ++ g e   ++l+AtsGdtg aa+e++
  lcl|NCBI__GCF_000024605.1:WP_015738594.1  87 EEIVpLKVLAPDVGILELWHGPTHAFKDLALTLLPHLMTRATQKlGLEkeiVILVATSGDTGKAALESF 155
                                               444345677789*******************99999999887742333455****************** PP

                                 TIGR00260  93 agkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke........klkl 152
                                               +  +  +++v+ P+ ++s + k +++t+  en  v+a++G+FDdaq  vk++f+d e         + +
  lcl|NCBI__GCF_000024605.1:WP_015738594.1 156 RDVPKTRIIVFFPSEGVSEIqKRQMITQEGENTFVVAVEGNFDDAQSGVKQLFGDPElrrkmesaGMTF 224
                                               ******************************************************7667778889899** PP

                                 TIGR00260 153 nsvNsinparieaqktyafeiveqlgk....espdkvvvpvpsgnfgailkGflekkelglpieklaia 217
                                               +s+Nsin++r++ q++y+f++ ++l +    ++ +++ ++vp gnfg+il+Gfl+ +++ lp++ l  a
  lcl|NCBI__GCF_000024605.1:WP_015738594.1 225 SSANSINWGRLLPQVVYYFSAYARLLRdkliRHGEEINFVVPTGNFGNILAGFLAREMG-LPVRRLILA 292
                                               ***********************99887778889********************99999.**8888777 PP

                                 TIGR00260 218 aegaadivrrflksgdlepkedk..eTlstAmdignpsnverale.larrslgnledlke......... 274
                                               a+ + ++++ f+++g ++ ++++   T+s++mdi+++sn er+l  +  r+ +++    +         
  lcl|NCBI__GCF_000024605.1:WP_015738594.1 293 ANAN-NVLTDFINTG-IYDRRRPfhRTISPSMDILISSNLERLLYlVTDRNAEKVR---Qwmtslartg 356
                                               7776.**********.777777778********************44444444444...34458999** PP

                                 TIGR00260 275 ...................svsdeeileaikklaeeegyllephtavavaalkklvekg...vs....a 317
                                                                   +sd+e+l aik ++ + gyll+pht+va  + ++  e++   +     +
  lcl|NCBI__GCF_000024605.1:WP_015738594.1 357 vyqidqatherikqvfwssWASDDETLAAIKDAYTRYGYLLDPHTGVAWHVFNRYREETgdsTKtvilS 425
                                               ******************999************************************99876226789* PP

                                 TIGR00260 318 tadpaKFeevve.altgnkl 336
                                               ta+p KF++ v  al  +kl
  lcl|NCBI__GCF_000024605.1:WP_015738594.1 426 TASPFKFARDVIrALAPEKL 445
                                               ********999878876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (500 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: 9.38
//
[ok]

This GapMind analysis is from Apr 10 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