Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Synpcc7942_0371 Synpcc7942_0371 homoserine O-succinyltransferase
Query= SwissProt::Q72X44 (301 letters) >FitnessBrowser__SynE:Synpcc7942_0371 Length = 299 Score = 314 bits (805), Expect = 1e-90 Identities = 148/295 (50%), Positives = 204/295 (69%) Query: 1 MPIIIDKDLPARKVLQEENIFVMTKERAETQDIRALKIAILNLMPTKQETEAQLLRLIGN 60 MPIII +DLPAR++L E++F + A QDIRAL++ +LNLMPTK TE Q+ R++ N Sbjct: 1 MPIIIPQDLPARRILDAESVFTLGDADARRQDIRALQVVVLNLMPTKVTTETQIARVLAN 60 Query: 61 TPLQLDVHLLHMESHLSRNVAQEHLTSFYKTFRDIENEKFDGLIITGAPVETLSFEEVDY 120 TPLQ+++ L+H S+ + EHL +FY TF I + +FDGLI+TGAPVETL + VDY Sbjct: 61 TPLQVELTLIHTASYQPTHTDPEHLRNFYSTFDQIRDRQFDGLIVTGAPVETLPWLAVDY 120 Query: 121 WEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEVREQHVKLL 180 W EL I+++S+ V S+L ICWGAQA L H +G++K L K FGVF H +R++ L+ Sbjct: 121 WSELTTILDWSREAVRSSLFICWGAQAALQHFHGIEKQTLPAKRFGVFWHHLRDRSSPLV 180 Query: 181 QGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYSC 240 +G D+ F P SRHTEV +++ +L +LA S EAG+HL+ + + + H EY Sbjct: 181 RGHDDDFLVPVSRHTEVIAAEVLAQSQLQILAESSEAGLHLLWDADQHRTYLFNHPEYDA 240 Query: 241 DTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQ 295 DTL +EY RDR+KGL I +P NY+ +D+PN+ P VRWRSH LL++NWLNY VYQ Sbjct: 241 DTLDREYRRDREKGLPIQLPLNYYPNDDPNQVPRVRWRSHAQLLYTNWLNYEVYQ 295 Lambda K H 0.319 0.136 0.403 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: 290 Number of extensions: 6 Number of successful extensions: 1 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: 301 Length of database: 299 Length adjustment: 27 Effective length of query: 274 Effective length of database: 272 Effective search space: 74528 Effective search space used: 74528 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate Synpcc7942_0371 Synpcc7942_0371 (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.27097.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-118 380.5 0.0 4.1e-118 380.3 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0371 Synpcc7942_0371 homoserine O-suc Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0371 Synpcc7942_0371 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.3 0.0 4.1e-118 4.1e-118 1 294 [. 1 295 [. 1 298 [. 0.99 Alignments for each domain: == domain 1 score: 380.3 bits; conditional E-value: 4.1e-118 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 mpi++p++lpa +l e++f ++ a+ qdir l+v++lnlmp k+ te+q+ r+l+n+plqv++tl lcl|FitnessBrowser__SynE:Synpcc7942_0371 1 MPIIIPQDLPARRILDAESVFTLGDADARRQDIRALQVVVLNLMPTKVTTETQIARVLANTPLQVELTL 69 9******************************************************************** PP TIGR01001 70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138 +++ s+++ +t ehl++fy ++++++dr+fdGlivtGapve l++ v+yw el+ il+ws+e v s+ lcl|FitnessBrowser__SynE:Synpcc7942_0371 70 IHTASYQPTHTDPEHLRNFYSTFDQIRDRQFDGLIVTGAPVETLPWLAVDYWSELTTILDWSREAVRSS 138 ********************************************************************* PP TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltd 206 l+icw+aqaal+ ++gi+k+tl+ k +Gv+ h+ ++++l+rg+dd fl+p sr++++ ++++ + ++ lcl|FitnessBrowser__SynE:Synpcc7942_0371 139 LFICWGAQAALQHFHGIEKQTLPAKRFGVFWHHLRdRSSPLVRGHDDDFLVPVSRHTEVIAAEVLAQSQ 207 **********************************98999****************************** PP TIGR01001 207 leilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpias 275 l+ilaes eag +l+ d+++ ++ hpeyd++tl ey rd ++gl ++ p nyyp+ddp++ p++ lcl|FitnessBrowser__SynE:Synpcc7942_0371 208 LQILAESSEAGLHLLWDADQHRTYLFNHPEYDADTLDREYRRDREKGLPIQLPLNYYPNDDPNQVPRVR 276 ********************************************************************* PP TIGR01001 276 wrshanllfanwlnyavyq 294 wrsha+ll++nwlny vyq lcl|FitnessBrowser__SynE:Synpcc7942_0371 277 WRSHAQLLYTNWLNYEVYQ 295 ******************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (299 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: 6.37 // [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