GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metA in Azospirillum brasilense Sp245

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate AZOBR_RS14010 AZOBR_RS14010 homoserine O-succinyltransferase

Query= SwissProt::G4RES5
         (306 letters)



>FitnessBrowser__azobra:AZOBR_RS14010
          Length = 307

 Score =  363 bits (932), Expect = e-105
 Identities = 162/305 (53%), Positives = 225/305 (73%), Gaps = 2/305 (0%)

Query: 1   MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60
           MPIRIP+ LPA   L+TEGV+VM ++ + RQDIRPL+FGLLNLMP+K RTETQ ARL+ +
Sbjct: 1   MPIRIPNDLPAFTALQTEGVMVMQEADAIRQDIRPLRFGLLNLMPDKIRTETQIARLLGN 60

Query: 61  TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120
           TPLQ++L+L+R+ + + ++T  D++  FY +WED R + FDGF++TGAP+  MPFE+V Y
Sbjct: 61  TPLQVELSLIRITNHVPRNTAADHMSAFYRSWEDARRETFDGFIITGAPVETMPFEEVSY 120

Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180
           W E+  + DWTQ++VH  + ICW AQAA+HH HGV ++ +  KA GV+RH+      P+L
Sbjct: 121 WDELCSVFDWTQSHVHACLNICWAAQAAVHHFHGVPKHLLPRKASGVFRHRNRAPASPYL 180

Query: 181 RGFSDDLAVPVSRYNDIDRQSLSPD--LDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238
            G SD + +PVSR+ ++    L P+  L +L+DS E G C+L+D  +R+ +M NH+EYD 
Sbjct: 181 CGLSDGVPIPVSRWTEVREDDLPPESGLRVLLDSPETGPCLLEDAAHRSLHMFNHIEYDT 240

Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298
            +L +EY RD+     TP+P   FP +DPS+ PENRWRSHAHLLF NWIN+IYQTTP+EL
Sbjct: 241 DTLRNEYVRDVAKDAATPVPHGYFPDDDPSQPPENRWRSHAHLLFANWINQIYQTTPFEL 300

Query: 299 EKVGT 303
            ++GT
Sbjct: 301 SRIGT 305


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: 373
Number of extensions: 17
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: 306
Length of database: 307
Length adjustment: 27
Effective length of query: 279
Effective length of database: 280
Effective search space:    78120
Effective search space used:    78120
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 AZOBR_RS14010 AZOBR_RS14010 (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.8531.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-107  345.9   0.0   1.4e-107  345.7   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS14010  AZOBR_RS14010 homoserine O-succi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS14010  AZOBR_RS14010 homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.7   0.0  1.4e-107  1.4e-107       1     300 [.       1     300 [.       1     301 [. 0.99

  Alignments for each domain:
  == domain 1  score: 345.7 bits;  conditional E-value: 1.4e-107
                                 TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 
                                               mpir+p++lpa   l+ e+++vm e  a+ qdirpl+  +lnlmp+ki+te+q+ rll+n+plqv++ l
  lcl|FitnessBrowser__azobra:AZOBR_RS14010   1 MPIRIPNDLPAFTALQTEGVMVMQEADAIRQDIRPLRFGLLNLMPDKIRTETQIARLLGNTPLQVELSL 69 
                                               9******************************************************************** PP

                                 TIGR01001  70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138
                                               +ri++++++nt ++h+  fy+++e+ + + fdG+i+tGapve ++fe+v+yw+el  +++w++++v ++
  lcl|FitnessBrowser__azobra:AZOBR_RS14010  70 IRITNHVPRNTAADHMSAFYRSWEDARRETFDGFIITGAPVETMPFEEVSYWDELCSVFDWTQSHVHAC 138
                                               ********************************************************************* PP

                                 TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltd 206
                                               l icwaaqaa++ ++g+pk+ l++k sGv++h+   + ++ l g+ d + +p sr++++ e+++   + 
  lcl|FitnessBrowser__azobra:AZOBR_RS14010 139 LNICWAAQAAVHHFHGVPKHLLPRKASGVFRHRNRaPASPYLCGLSDGVPIPVSRWTEVREDDLPPESG 207
                                               ********************************998799******************************* PP

                                 TIGR01001 207 leilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpias 275
                                               l +l++s e+g  l+    +r + +  h eyd +tlr+eyvrdv ++   ++p+ y+p+ddp++ p   
  lcl|FitnessBrowser__azobra:AZOBR_RS14010 208 LRVLLDSPETGPCLLEDAAHRSLHMFNHIEYDTDTLRNEYVRDVAKDAATPVPHGYFPDDDPSQPPENR 276
                                               ********************************************************************* PP

                                 TIGR01001 276 wrshanllfanwlnyavyqktpydl 300
                                               wrsha+llfanw+n ++yq+tp++l
  lcl|FitnessBrowser__azobra:AZOBR_RS14010 277 WRSHAHLLFANWIN-QIYQTTPFEL 300
                                               **************.69******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (307 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: 9.15
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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