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.804.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 9.93 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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