Alignments for a candidate for metA in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for metA in Sinorhizobium medicae WSM419

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_024324237.1 SMED_RS15205 homoserine O-succinyltransferase

Query= SwissProt::G4RES5
         (306 letters)



>NCBI__GCF_000017145.1:WP_024324237.1
          Length = 308

 Score =  380 bits (975), Expect = e-110
 Identities = 174/308 (56%), Positives = 232/308 (75%), Gaps = 2/308 (0%)

Query: 1   MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60
           MPI+IPD LPA +TL  EGV +M ++ + RQDIRPLQ GLLNLMPNK +TE Q ARLI +
Sbjct: 1   MPIKIPDTLPAFETLVHEGVRLMTETEAIRQDIRPLQIGLLNLMPNKIKTEVQMARLIGA 60

Query: 61  TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120
           TPLQ++LTLVRV     K+TPE++L  FY T+E+V A+KFDGF++TGAP+  + +E+V Y
Sbjct: 61  TPLQVELTLVRVNGHRPKNTPEEHLLAFYETFEEVEARKFDGFIITGAPVETLEYEEVTY 120

Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180
           W E+  I DWT TNVH T+ +CWGA AA++H HG+ +Y ++ KAFGVYRH+ L     +L
Sbjct: 121 WKELQRIFDWTTTNVHSTLNVCWGAMAAIYHFHGIPKYPLKEKAFGVYRHQNLKPSSVYL 180

Query: 181 RGFSDDLAVPVSRYNDIDRQSLS--PDLDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238
            GFSDD AVPVSR+ ++ R  +   PDL+IL++S E+G+C++ ++K    YM NH+EYD+
Sbjct: 181 NGFSDDFAVPVSRWTEVRRADIDRVPDLEILMESKEMGVCLVHEKKGNRLYMFNHVEYDS 240

Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298
           TSL++EY RD++AG+   LP + FP ND +  P+NRWRSHAHL F NWINEIYQTTPYE 
Sbjct: 241 TSLSEEYFRDVDAGVPIKLPHDYFPHNDSALPPQNRWRSHAHLFFGNWINEIYQTTPYEP 300

Query: 299 EKVGTGEW 306
            K+G G +
Sbjct: 301 AKIGAGAY 308


Lambda     K      H
   0.321    0.137    0.431 

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: 342
Number of extensions: 15
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: 306
Length of database: 308
Length adjustment: 27
Effective length of query: 279
Effective length of database: 281
Effective search space:    78399
Effective search space used:    78399
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: 48 (23.1 bits)

Align candidate WP_024324237.1 SMED_RS15205 (homoserine O-succinyltransferase)
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))

# 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/TIGR01001.hmm
# target sequence database:        /tmp/gapView.3595659.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01001  [M=301]
Accession:   TIGR01001
Description: metA: homoserine O-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-118  379.9   0.1   6.5e-118  379.6   0.1    1.0  1  NCBI__GCF_000017145.1:WP_024324237.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017145.1:WP_024324237.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.6   0.1  6.5e-118  6.5e-118       1     299 [.       1     299 [.       1     300 [. 0.99

  Alignments for each domain:
  == domain 1  score: 379.6 bits;  conditional E-value: 6.5e-118
                             TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllrid 73 
                                           mpi++pd lpa e l +e++ +mte  a+ qdirpl++ +lnlmp+ki+te q+ rl++ +plqv++tl+r++
  NCBI__GCF_000017145.1:WP_024324237.1   1 MPIKIPDTLPAFETLVHEGVRLMTETEAIRQDIRPLQIGLLNLMPNKIKTEVQMARLIGATPLQVELTLVRVN 73 
                                           9************************************************************************ PP

                             TIGR01001  74 srkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaq 146
                                            +++kntp+ehl  fy+++eev+ rkfdG+i+tGapve le+e+v yw+el+ i++w+ +nv stl +cw+a+
  NCBI__GCF_000017145.1:WP_024324237.1  74 GHRPKNTPEEHLLAFYETFEEVEARKFDGFIITGAPVETLEYEEVTYWKELQRIFDWTTTNVHSTLNVCWGAM 146
                                           ************************************************************************* PP

                             TIGR01001 147 aalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagv 218
                                           aa++ ++gipk+ l+ek +Gvy+h+ + ++++ l+gf d f +p sr++++ +++i+ ++dleil+es+e+gv
  NCBI__GCF_000017145.1:WP_024324237.1 147 AAIYHFHGIPKYPLKEKAFGVYRHQNLkPSSVYLNGFSDDFAVPVSRWTEVRRADIDRVPDLEILMESKEMGV 219
                                           *************************9978999***************************************** PP

                             TIGR01001 219 ylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnya 291
                                            l+ +k+  ++++  h eyd  +l +ey+rdv++g+ ++ p++y+p++d+   p   wrsha+l+f nw+n  
  NCBI__GCF_000017145.1:WP_024324237.1 220 CLVHEKKGNRLYMFNHVEYDSTSLSEEYFRDVDAGVPIKLPHDYFPHNDSALPPQNRWRSHAHLFFGNWIN-E 291
                                           **********************************************************************9.7 PP

                             TIGR01001 292 vyqktpyd 299
                                           +yq+tpy+
  NCBI__GCF_000017145.1:WP_024324237.1 292 IYQTTPYE 299
                                           9******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (308 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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