Alignments for a candidate for metX in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Herbaspirillum seropedicae SmR1

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate HSERO_RS00455 HSERO_RS00455 homoserine O-acetyltransferase

Query= SwissProt::Q12XS2
         (488 letters)



>FitnessBrowser__HerbieS:HSERO_RS00455
          Length = 379

 Score =  376 bits (965), Expect = e-109
 Identities = 184/365 (50%), Positives = 245/365 (67%), Gaps = 4/365 (1%)

Query: 5   SVGIVATNYHTIEGEFQLEGGHTLKNIRLAYETYGNLNKEKSNAILVCHALTGDAHAAGR 64
           S+GIV+           L+GG  L +  L YETYG LN +KSNA+LVCHAL    H AG 
Sbjct: 2   SIGIVSPQVMHFAEPLPLQGGSALADYSLTYETYGTLNADKSNAVLVCHALNASHHVAGV 61

Query: 65  HSDDDKKPGWWDDIIGPGKALDTDRYFVLCSNVLGGCKGTTGPASLDPDTGRQYGITFPV 124
           ++DD    GWWD+++GPGK+LDTDR+FV+  N LG C G+TGP   +P TG+ YG  FPV
Sbjct: 62  YADDPDNVGWWDNMVGPGKSLDTDRFFVIGVNNLGSCFGSTGPMHANPATGKPYGADFPV 121

Query: 125 ITIRDMVNVQKRLIDHMGITTLFAVVGGSMGGMQTLQWCVAYPELVKKAVVIASTAVSSP 184
           +T+ D VN Q RL D +GIT   AV+GGS+GGMQ L W + YP+ ++  +VIAST   S 
Sbjct: 122 VTVEDWVNAQARLADRLGITCFAAVMGGSLGGMQALAWSMMYPDRLRHCLVIASTPKLSA 181

Query: 185 QQIAFNEVGRNAIISDPDWNGGDYY-EGEPPVNGLSTARMIAHITYLSDASMHEKFGRRL 243
           Q IAFN+V R AI++DP ++GGD+Y  G  P NGL  ARM+ HITYLSD  M EKFGR L
Sbjct: 182 QNIAFNDVARQAILTDPQYHGGDFYAHGVVPKNGLRVARMVGHITYLSDDDMAEKFGRDL 241

Query: 244 QQGESYKFDMSNDFQVGSYLKYQGDTFTGRFDANSYLYATKAVDYFD--LSMNGSLAEGL 301
           + G+ Y+F    DF++ SYL+YQGD F+  FDAN+YL  TKA+DYFD      G LA+ L
Sbjct: 242 RSGQ-YQFGYGVDFEIESYLRYQGDKFSTYFDANTYLLITKALDYFDPAREFGGDLAKAL 300

Query: 302 KYVQAKMLVISITSDWLYSPYHSKKIVEGLTVKEHDVSYREIESSYGHDAFLLESGQINY 361
              +AK L++S T+DW +SP  S+++V+ L   +  VSY EI++ +GHDAFLL+  +   
Sbjct: 301 ACTKAKFLLVSFTTDWRFSPERSREMVQALVANKRRVSYAEIDAPHGHDAFLLDDARYMK 360

Query: 362 VIHNF 366
           V+  +
Sbjct: 361 VVREY 365


Lambda     K      H
   0.318    0.134    0.397 

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: 537
Number of extensions: 26
Number of successful extensions: 4
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: 488
Length of database: 379
Length adjustment: 32
Effective length of query: 456
Effective length of database: 347
Effective search space:   158232
Effective search space used:   158232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate HSERO_RS00455 HSERO_RS00455 (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.28705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     2e-143  463.7   0.0   2.3e-143  463.5   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS00455  HSERO_RS00455 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS00455  HSERO_RS00455 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.5   0.0  2.3e-143  2.3e-143       3     349 ..      15     365 ..      13     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 463.5 bits;  conditional E-value: 2.3e-143
                                  TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgral 68 
                                                e+l l+ G+ l +++++y+tyGtlna+++NavlvcHal +s+hvag + ++ +  GWWd+++Gpg++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS00455  15 EPLPLQGGSALADYSLTYETYGTLNADKSNAVLVCHALNASHHVAGVYADDPDnvGWWDNMVGPGKSL 82 
                                                7899******************************************998776678************* PP

                                  TIGR01392  69 dtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgS 136
                                                dt+r+fv+++N+lGsc GstgP+ +np+tgkpyga+fP+vt++D+v+aq++l+d+Lg++ +aav+GgS
  lcl|FitnessBrowser__HerbieS:HSERO_RS00455  83 DTDRFFVIGVNNLGSCFGSTGPMHANPATGKPYGADFPVVTVEDWVNAQARLADRLGITCFAAVMGGS 150
                                                ******************************************************************** PP

                                  TIGR01392 137 lGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLal 203
                                                lGGmqal w+++yp+r+++++v+a+++++saq+iafn+v+rqail+Dp+y++G+++ ++  P++GL++
  lcl|FitnessBrowser__HerbieS:HSERO_RS00455 151 LGGMQALAWSMMYPDRLRHCLVIASTPKLSAQNIAFNDVARQAILTDPQYHGGDFYAHGvVPKNGLRV 218
                                                **********************************************************99******** PP

                                  TIGR01392 204 ARmlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldt 271
                                                ARm++++tY+s+++++e+fgr+ +s  ++++ +  +f++esylryqg+kf + FdAn+Yll+tkald+
  lcl|FitnessBrowser__HerbieS:HSERO_RS00455 219 ARMVGHITYLSDDDMAEKFGRDLRSG-QYQFGYGVDFEIESYLRYQGDKFSTYFDANTYLLITKALDY 285
                                                ************************99.77999************************************ PP

                                  TIGR01392 272 hdlargrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFll 337
                                                +d ar+  ++l++al+ +ka++l+v++++D++f++e+++e+++al a+k +  yaei+ ++GHDaFll
  lcl|FitnessBrowser__HerbieS:HSERO_RS00455 286 FDPAREFGGDLAKALACTKAKFLLVSFTTDWRFSPERSREMVQALVANKRRvsYAEIDAPHGHDAFLL 353
                                                *********************************************99988888*************** PP

                                  TIGR01392 338 ekekveeliref 349
                                                +++++++++re+
  lcl|FitnessBrowser__HerbieS:HSERO_RS00455 354 DDARYMKVVREY 365
                                                *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (379 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: 10.90
//
[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