Align Succinylglutamate desuccinylase; EC 3.5.1.96 (uncharacterized)
to candidate 6937552 Sama_1708 succinylglutamate desuccinylase (RefSeq)
Query= curated2:A4Y6M4 (344 letters) >FitnessBrowser__SB2B:6937552 Length = 348 Score = 502 bits (1293), Expect = e-147 Identities = 254/347 (73%), Positives = 283/347 (81%), Gaps = 4/347 (1%) Query: 1 MLQALLDSKDFLALTLAHPEQFDGEFSFNLGDHTQVEVWDTGVIVFEPIQ-NEGKDIVLS 59 ML L KDFL LTL++PE D L HT V +WDTGV+VFEP+ N KDIVLS Sbjct: 1 MLNLLQGCKDFLHLTLSNPEHLDPIAPQPLYGHTLVSLWDTGVLVFEPVDGNSHKDIVLS 60 Query: 60 CGVHGNETAPIELCNSLIKQLLQQKIIAKQRTLFLIGNPLAINNGTRIIDENMNRLFSGE 119 GVHGNETAPIELCN LI+ +L+ ++ K+R LFLIGNP AINNGTRI+DENMNRLFSGE Sbjct: 61 SGVHGNETAPIELCNGLIQDVLEGRLQVKERVLFLIGNPAAINNGTRIVDENMNRLFSGE 120 Query: 120 HSNPPGLVNPERVRAKKLEAYVDRFFTAAAD---GRQRIHYDLHTAMRASKHEKFAIYPY 176 HS PGL NPERVRAKKLE YV RFF A+ GRQRIHYDLHTA+R SKHEKFAIYPY Sbjct: 121 HSRGPGLSNPERVRAKKLETYVTRFFEKGAEKGEGRQRIHYDLHTAIRGSKHEKFAIYPY 180 Query: 177 RPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSERYGADAFTIELGKVYPMGQNDM 236 RPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSE + ADAFTIELGKVYPMGQNDM Sbjct: 181 RPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSELFRADAFTIELGKVYPMGQNDM 240 Query: 237 TRFIATHEMFMRLITAKPLELDAFDADKVNLYQVCRVINKHFDDFEFTFATDVENFRSFP 296 ++F T EMF RLI A+PLEL FD +VNLYQVCRVINK DDFEFTF+TDVENF +FP Sbjct: 241 SKFANTREMFKRLICAEPLELAPFDETQVNLYQVCRVINKEVDDFEFTFSTDVENFSAFP 300 Query: 297 KGFVLAREGGQEIKVEHEFESVVFPNAKVPIGNRTVICLIPAVNADV 343 +G V+AR+GG++I VE E E+VVFPNAKVP+G RTVI L+PAVN V Sbjct: 301 RGHVIARQGGKDILVEQEAEAVVFPNAKVPVGQRTVIMLVPAVNPHV 347 Lambda K H 0.323 0.139 0.412 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: 464 Number of extensions: 10 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: 344 Length of database: 348 Length adjustment: 29 Effective length of query: 315 Effective length of database: 319 Effective search space: 100485 Effective search space used: 100485 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 bits)
Align candidate 6937552 Sama_1708 (succinylglutamate desuccinylase (RefSeq))
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))
# 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/TIGR03242.hmm # target sequence database: /tmp/gapView.11770.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03242 [M=319] Accession: TIGR03242 Description: arg_catab_astE: succinylglutamate desuccinylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-107 345.5 0.0 1.8e-107 345.3 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6937552 Sama_1708 succinylglutamate desu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937552 Sama_1708 succinylglutamate desuccinylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 345.3 0.0 1.8e-107 1.8e-107 1 319 [] 10 340 .. 10 340 .. 0.91 Alignments for each domain: == domain 1 score: 345.3 bits; conditional E-value: 1.8e-107 TIGR03242 1 dflaltlekkep...evtqgeaknvklrwldeGvlelePe.aeaekslvisaGihGnetaPielleqllsdiaagkl 73 dfl+ltl++ e + q + + d+Gvl eP + +k++v+s+G+hGnetaPiel + l++d+++g+l lcl|FitnessBrowser__SB2B:6937552 10 DFLHLTLSNPEHldpIAPQPLYGHTLVSLWDTGVLVFEPVdGNSHKDIVLSSGVHGNETAPIELCNGLIQDVLEGRL 86 677888776543311333333455556799*********9456789******************************* PP TIGR03242 74 qlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqele..eskeklRaeeLeqvveaffeagkasea...ryhyDl 145 q+k r+L+++Gnpaa+++g R ++e++nRlf+G++ + + e+ Ra++Le +v++ffe+g + + r hyDl lcl|FitnessBrowser__SB2B:6937552 87 QVKERVLFLIGNPAAINNGTRIVDENMNRLFSGEHSRGPglSNPERVRAKKLETYVTRFFEKGAEKGEgrqRIHYDL 163 ***********************************8865225579*****************998765677****** PP TIGR03242 146 htaiRasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendl 221 htaiR+sk+ekfa++Py+ ++ f+ e++ +laa+++d+vl+h+e+++tfs+fsse + a+a+t+elGk+ P G+nd+ lcl|FitnessBrowser__SB2B:6937552 164 HTAIRGSKHEKFAIYPYRpGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSELFRADAFTIELGKVYPMGQNDM 240 ***************************************************************************** PP TIGR03242 222 sqfqaitealralisdeaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrvee 296 s+f+++ e ++li e + ++ +++l++v + i k+ d+fe+ + d++nf+ f++G+++a++ ++ ve+ lcl|FitnessBrowser__SB2B:6937552 241 SKFANTREMFKRLICAEPLELAPFDetQVNLYQVCRVINKEVDDFEFTFSTDVENFSAFPRGHVIARQGGKDILVEQ 317 ***************99887776665599************************************************ PP TIGR03242 297 eeerilfPnakvanGlRaglllv 319 e+e ++fPnakv G+R +++lv lcl|FitnessBrowser__SB2B:6937552 318 EAEAVVFPNAKVPVGQRTVIMLV 340 *********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (319 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.83 // [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