Alignments for a candidate for metX in Caminibacter mediatlanticus TB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Caminibacter mediatlanticus TB-2

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_007472882.1 CMTB2_RS00345 homoserine O-acetyltransferase

Query= SwissProt::B9L9I6
         (368 letters)



>NCBI__GCF_000170735.1:WP_007472882.1
          Length = 368

 Score =  648 bits (1671), Expect = 0.0
 Identities = 319/368 (86%), Positives = 342/368 (92%), Gaps = 4/368 (1%)

Query: 1   MKIETKIAKFTKPLYLESGRILEPWQIIYETYGELNEKKDNVILITHALSGSHHAAGMYE 60
           M I+TKIAKFTKPLYLESGRILEPWQIIYETYGELNE K N ILITHALSGSHHAAG Y+
Sbjct: 1   MNIKTKIAKFTKPLYLESGRILEPWQIIYETYGELNEDKSNAILITHALSGSHHAAGWYK 60

Query: 61  GDRKPGWWDGLIGDGKAIDTTKYFVISTNVIGSCFGSTSPMSPIHPGSSERYRLKFPVVT 120
           GDRKPGWWDGLIGD KAIDTTKYFVI TNVIGSCFGSTSPMSPI+PGS+ERYRLKFPV+T
Sbjct: 61  GDRKPGWWDGLIGDSKAIDTTKYFVICTNVIGSCFGSTSPMSPIYPGSNERYRLKFPVIT 120

Query: 121 IKDMVKAQKILLDSLGIRHLKAIVGGSMGGMQALRFAVDFPGFCENIIPIATTYQTKPYV 180
           IKDMVKAQKILLDSLGI+ LKA+VGGSMGGMQALRF VDFPGF ENIIPIATTYQT+PYV
Sbjct: 121 IKDMVKAQKILLDSLGIKKLKAVVGGSMGGMQALRFGVDFPGFVENIIPIATTYQTRPYV 180

Query: 181 IAINKSMIEAIRADSEFKNGNYDPDIIKQNGLKGLAAARMIGYLNYISPKTFERKFGREY 240
           IAINKSMIEAIRAD EFKNGNY  +I K+  LKGLA ARMIGYLNYISPKTF++KFGREY
Sbjct: 181 IAINKSMIEAIRADCEFKNGNY--EIGKE--LKGLAVARMIGYLNYISPKTFDKKFGREY 236

Query: 241 VKTDGMFELFGRFQVESYLEYNGAMFPKWFDPLSYIYILKAISLFDISRGFVSLEDAFSQ 300
           VKTDGMFELFGRFQVESYLEYNGAMFPKWFD LSYIY+LKAISLFDI RGF SL++AFS 
Sbjct: 237 VKTDGMFELFGRFQVESYLEYNGAMFPKWFDALSYIYLLKAISLFDIGRGFNSLDEAFSN 296

Query: 301 IKDKLHLISFSGDTLFFPEEMRDIKNYMDKVGGKCNYFEINSDYGHDSFLVELEKFDFII 360
           IKDKL LISFSGDTLFFPEEMR+IK YMDKVGG+C Y+EI+SDYGHDSFLVE++KF  +I
Sbjct: 297 IKDKLFLISFSGDTLFFPEEMREIKKYMDKVGGRCQYYEIDSDYGHDSFLVEIDKFSDLI 356

Query: 361 SDILKGEV 368
           SDILKGE+
Sbjct: 357 SDILKGEM 364


Lambda     K      H
   0.322    0.141    0.422 

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: 602
Number of extensions: 17
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: 368
Length of database: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_007472882.1 CMTB2_RS00345 (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.28122.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.9e-124  399.2   0.0     9e-124  399.0   0.0    1.0  1  lcl|NCBI__GCF_000170735.1:WP_007472882.1  CMTB2_RS00345 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000170735.1:WP_007472882.1  CMTB2_RS00345 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.0   0.0    9e-124    9e-124       2     350 ..      11     360 ..      10     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 399.0 bits;  conditional E-value: 9e-124
                                 TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgrald 69 
                                               +++l+lesG +l+  ++ y+tyG+ln++++Na+l+ Hal+gs+h+ag ++ ++k GWWd l+G+ +a+d
  lcl|NCBI__GCF_000170735.1:WP_007472882.1  11 TKPLYLESGRILEPWQIIYETYGELNEDKSNAILITHALSGSHHAAGWYKGDRKpGWWDGLIGDSKAID 79 
                                               589*********************************************9998888************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPls.inpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSl 137
                                               t++yfv+c+Nv+Gsc Gst+P+s i p ++++y+ +fP++ti+D+vkaqk lldsLg++kl+avvGgS+
  lcl|NCBI__GCF_000170735.1:WP_007472882.1  80 TTKYFVICTNVIGSCFGSTSPMSpIYPGSNERYRLKFPVITIKDMVKAQKILLDSLGIKKLKAVVGGSM 148
                                               **********************9567899**************************************** PP

                                 TIGR01392 138 GGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARm 206
                                               GGmqal + ++ p +v++i+++at+ ++ +  ia+n+ +++ai++D e+++G+y+  ++  kGLa+ARm
  lcl|NCBI__GCF_000170735.1:WP_007472882.1 149 GGMQALRFGVDFPGFVENIIPIATTYQTRPYVIAINKSMIEAIRADCEFKNGNYEI-GKELKGLAVARM 216
                                               *******************************************************9.7789******** PP

                                 TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                               ++ l Y s ++++++fgre  +++  +++l  +f+vesyl+y+g  f + FdA sY++l ka+  +d++
  lcl|NCBI__GCF_000170735.1:WP_007472882.1 217 IGYLNYISPKTFDKKFGREYVKTDG-MFELFGRFQVESYLEYNGAMFPKWFDALSYIYLLKAISLFDIG 284
                                               ********************99965.67799************************************** PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                               rg  +sl ea+++ik + ++++++ D+lf +ee +e++k + +++ +  y+ei+s++GHD+Fl+e +k+
  lcl|NCBI__GCF_000170735.1:WP_007472882.1 285 RG-FNSLDEAFSNIKDKLFLISFSGDTLFFPEEMREIKKYMDKVGGRcqYYEIDSDYGHDSFLVEIDKF 352
                                               **.8***************************************998889******************** PP

                                 TIGR01392 343 eelirefl 350
                                               ++li+++l
  lcl|NCBI__GCF_000170735.1:WP_007472882.1 353 SDLISDIL 360
                                               ****9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (368 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: 9.45
//
[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