Alignments for a candidate for metX in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Halomonas desiderata SP1

Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_086510438.1 BZY95_RS13465 homoserine O-acetyltransferase

Query= curated2:Q1QQD3
         (399 letters)



>NCBI__GCF_002151265.1:WP_086510438.1
          Length = 385

 Score =  400 bits (1028), Expect = e-116
 Identities = 199/372 (53%), Positives = 254/372 (68%), Gaps = 4/372 (1%)

Query: 24  TSQVAMFAGDQPLPLDCGIDLAPFQIAYQTYGELNAGKSNAILVCHALTGDQHVANVHPV 83
           T Q A F  D PL L CG  L  + + Y+TYG LNA +SNA+L+CHAL+G  H A  H  
Sbjct: 13  TPQTAHF--DDPLALACGRTLPAYDLVYETYGTLNAERSNAVLICHALSGHHHAAGYHDA 70

Query: 84  TG-KPGWWVTLVGPGKPLDTDKYFVICSNVIGGCMGSTGPASTNPATGTVWGLDFPVITI 142
              KPGWW   +GPGK +DT+++FV+  N +GGC GSTGP STNPATG  WG DFP++T+
Sbjct: 71  DERKPGWWDAHIGPGKSIDTNRFFVVSLNNLGGCHGSTGPISTNPATGRQWGPDFPMVTV 130

Query: 143 PDMVRAQAMLIDRLGIDTLFSVVGGSMGGMQVLQWCVAYPQRVFSALPIACSTRHSAQNI 202
            D V +QA L DRLGI+   + +GGS+GGMQVLQW   YP+RV +A+ IA + + SAQNI
Sbjct: 131 SDWVHSQARLADRLGIERFAAAIGGSLGGMQVLQWTRLYPERVANAVIIAATPKLSAQNI 190

Query: 203 AFHELGRQAVMADPDWRDGRYVEQGTYPHRGLGVARMAAHITYLSDAALHRKFGRRMQDR 262
           AF+E+ RQA+ +DPD+ DG Y E GT P RGL +ARM  HITYLS+ A+  KFGR ++  
Sbjct: 191 AFNEVARQAIRSDPDFHDGWYAEHGTAPRRGLKLARMVGHITYLSEDAMGSKFGRDLRSE 250

Query: 263 DLPTFSFDADFQVESYLRHQGSSFVERFDANSYLYLTRAMDYFDIAADHNGVLAAAFRDT 322
           DL  F +D +FQVESYLR+QG +F   FDAN+YL +T+A+DYFD AA+H GVLA A    
Sbjct: 251 DL-NFGYDVEFQVESYLRYQGDTFSTAFDANTYLLMTKALDYFDPAAEHGGVLAEAVAPC 309

Query: 323 RTRFCVVSFTSDWLFPTSESRATVHALNAGGARVSFAEIETDRGHDAFLLDLPEFFDIAH 382
           +  F VVSFTSDW FP S SR   +AL   G RVS+  I++  GHDAFLL  P +  +  
Sbjct: 310 QGPFLVVSFTSDWRFPPSRSRELANALIRAGKRVSYVNIDSPHGHDAFLLPEPRYQAVFA 369

Query: 383 AFLVSAGKTRGL 394
           AF+    +  GL
Sbjct: 370 AFMSRVARELGL 381


Lambda     K      H
   0.323    0.136    0.427 

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: 500
Number of extensions: 18
Number of successful extensions: 3
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: 399
Length of database: 385
Length adjustment: 31
Effective length of query: 368
Effective length of database: 354
Effective search space:   130272
Effective search space used:   130272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate WP_086510438.1 BZY95_RS13465 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))

# 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/TIGR01392.hmm
# target sequence database:        /tmp/gapView.5207.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01392  [M=351]
Accession:   TIGR01392
Description: homoserO_Ac_trn: homoserine O-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-145  468.2   0.0   9.8e-145  468.0   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510438.1  BZY95_RS13465 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510438.1  BZY95_RS13465 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.0   0.0  9.8e-145  9.8e-145       3     350 ..      21     372 ..      19     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 468.0 bits;  conditional E-value: 9.8e-145
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgrald 69 
                                               ++l l +G +l+ ++++y+tyGtlnaer+Navl+cHal+g++h+ag++d++++  GWWd  +Gpg+++d
  lcl|NCBI__GCF_002151265.1:WP_086510438.1  21 DPLALACGRTLPAYDLVYETYGTLNAERSNAVLICHALSGHHHAAGYHDADERkpGWWDAHIGPGKSID 89 
                                               789*********************************************9888789************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               t+r+fvv+lN+lG+c+GstgP+s+np+tg+++g++fP+vt+ D+v+ q++l+d+Lg+e++aa +GgSlG
  lcl|NCBI__GCF_002151265.1:WP_086510438.1  90 TNRFFVVSLNNLGGCHGSTGPISTNPATGRQWGPDFPMVTVSDWVHSQARLADRLGIERFAAAIGGSLG 158
                                               ********************************************************************* PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARm 206
                                               Gmq+l+w+  yperv ++v +a+++++saq+iafnev+rqai+sDp+++dG+yae++ +P++GL+lARm
  lcl|NCBI__GCF_002151265.1:WP_086510438.1 159 GMQVLQWTRLYPERVANAVIIAATPKLSAQNIAFNEVARQAIRSDPDFHDGWYAEHGtAPRRGLKLARM 227
                                               *********************************************************9*********** PP

                                 TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                               ++++tY+se+++ ++fgr+ +se +l++ ++ ef+vesylryqg++f + FdAn+Yll+tkald++d a
  lcl|NCBI__GCF_002151265.1:WP_086510438.1 228 VGHITYLSEDAMGSKFGRDLRSE-DLNFGYDVEFQVESYLRYQGDTFSTAFDANTYLLMTKALDYFDPA 295
                                               *******************9998.88999**************************************** PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                               +++ + l+ea++ ++ p+lvv+++sD++f++++++ela+al +a+++  y++i+s++GHDaFll + ++
  lcl|NCBI__GCF_002151265.1:WP_086510438.1 296 AEHGGVLAEAVAPCQGPFLVVSFTSDWRFPPSRSRELANALIRAGKRvsYVNIDSPHGHDAFLLPEPRY 364
                                               ******************************************9999999******************99 PP

                                 TIGR01392 343 eelirefl 350
                                               +++ ++f+
  lcl|NCBI__GCF_002151265.1:WP_086510438.1 365 QAVFAAFM 372
                                               99988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (385 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: 9.85
//
[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