Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 6937471 Sama_1627 arginine N-succinyltransferase (RefSeq)
Query= reanno::ANA3:7023381 (339 letters) >FitnessBrowser__SB2B:6937471 Length = 348 Score = 336 bits (861), Expect = 6e-97 Identities = 172/341 (50%), Positives = 232/341 (68%), Gaps = 4/341 (1%) Query: 1 MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL 60 ML+IRPIQ DF++L +A ESG GFTSLP+ L HKIA +E SF ID P D+GYL Sbjct: 1 MLLIRPIQGSDFQALMTMARESGAGFTSLPLCERKLTHKIAHSEESFAADIDAPGDQGYL 60 Query: 61 MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA 120 VLEDT T E++G IEA+VG+ YH+ T V+ +++++ N VE LTL +DYTG Sbjct: 61 FVLEDTDTGEILGASGIEASVGLGSPLYHFHKSTVVHQCKELDIFNPVEVLTLGNDYTGV 120 Query: 121 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL 180 E+CTLFLRE YR G NGR LS+ RF+F+A+H KRF + VIAEMRG +D +G PF+ WL Sbjct: 121 TEICTLFLREPYRVGLNGRFLSKVRFMFMAEHPKRFSQLVIAEMRGAADENGQPPFWGWL 180 Query: 181 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240 ++ F ++F +ADYL G+G K F+A++MPR P+YV LLPE A+ IG+VH NT PAL LL Sbjct: 181 RETFFNMEFSKADYLIGVGNKGFIADLMPRYPIYVDLLPEAARNTIGQVHENTVPALKLL 240 Query: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDK---QFIVSNTQL 297 + EGF RGYVD+FD GPTVE +L I++VR+S + V I + P K V N Sbjct: 241 ENEGFMHRGYVDLFDAGPTVEAQLKQIKSVRQSHRVKVVISQNPAEHKGEFHLAVCNCDS 300 Query: 298 ANYRAT-SACLAVDDKTEQVVISPELAEGLLLAKGDQIRIL 337 +RAT S ++ +T +++SP +A+ L +A+GD +R L Sbjct: 301 KAFRATVSDECRLEPETHSILMSPAMADVLNVAEGDLVRYL 341 Lambda K H 0.322 0.138 0.401 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: 350 Number of extensions: 11 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: 339 Length of database: 348 Length adjustment: 29 Effective length of query: 310 Effective length of database: 319 Effective search space: 98890 Effective search space used: 98890 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: 49 (23.5 bits)
Align candidate 6937471 Sama_1627 (arginine N-succinyltransferase (RefSeq))
to HMM TIGR03244 (astA: arginine N-succinyltransferase (EC 2.3.1.109))
# 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.carbon/TIGR03244.hmm # target sequence database: /tmp/gapView.18426.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03244 [M=336] Accession: TIGR03244 Description: arg_catab_AstA: arginine N-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-136 438.9 0.0 5.6e-136 438.7 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6937471 Sama_1627 arginine N-succinyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937471 Sama_1627 arginine N-succinyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.7 0.0 5.6e-136 5.6e-136 1 335 [. 3 342 .. 3 343 .. 0.96 Alignments for each domain: == domain 1 score: 438.7 bits; conditional E-value: 5.6e-136 TIGR03244 1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfage.leraeegylfvledtetgkvvGvsaiea 76 ++rp++ sd++al+++a+e+G G+tslp e +l+++i+++e+sfa + +++++gylfvledt+tg++ G s+iea lcl|FitnessBrowser__SB2B:6937471 3 LIRPIQGSDFQALMTMARESGAGFTSLPLCERKLTHKIAHSEESFAADiDAPGDQGYLFVLEDTDTGEILGASGIEA 79 69**********************************************44689************************ PP TIGR03244 77 avGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaefkerf 153 vGl p y+++ ++vvh++kel+i++ +e+l+l nd+tg++e+Ctlfl+e yr +lnG++lsk+rf+f+ae+++rf lcl|FitnessBrowser__SB2B:6937471 80 SVGLGSPLYHFHKSTVVHQCKELDIFNPVEVLTLGNDYTGVTEICTLFLREPYRVGLNGRFLSKVRFMFMAEHPKRF 156 ***************************************************************************** PP TIGR03244 154 skkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhekt 230 s+ +iaemrG +de+G+ PfW +l + ff+++fskadyl g+G+k fia+lmP++Piyvdll+++a++ ig+vhe+t lcl|FitnessBrowser__SB2B:6937471 157 SQLVIAEMRGAADENGQPPFWGWLRETFFNMEFSKADYLIGVGNKGFIADLMPRYPIYVDLLPEAARNTIGQVHENT 233 ***************************************************************************** PP TIGR03244 231 kPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepyl.vanekledfrvvlves 306 +Pal+lle+eG+ ++gyvd+fdaGpt+ea++++i++vr+s++v+v +++ ae+++e +l v+n + + fr+++ + lcl|FitnessBrowser__SB2B:6937471 234 VPALKLLENEGFMHRGYVDLFDAGPTVEAQLKQIKSVRQSHRVKVVISQNPAEHKGEFHLaVCNCDSKAFRATVSDE 310 *******************************************9999877777666655449**********98765 PP TIGR03244 307 s...ldaeelvlsaeeakalkveeGdkvrvva 335 +++++++s++ a++l+v eGd vr ++ lcl|FitnessBrowser__SB2B:6937471 311 CrlePETHSILMSPAMADVLNVAEGDLVRYLN 342 333388999********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (336 nodes) Target sequences: 1 (348 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: 12.14 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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