Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate PP_4475 PP_4475 succinylglutamate desuccinylase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977 (336 letters) >FitnessBrowser__Putida:PP_4475 Length = 335 Score = 509 bits (1312), Expect = e-149 Identities = 257/335 (76%), Positives = 292/335 (87%), Gaps = 1/335 (0%) Query: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 MLALGKLLELTL EPAEKTQ+T +G R+RWL EGALEVRP E+ D GLDLLLSAGIHG Sbjct: 1 MLALGKLLELTLTDHEPAEKTQVTPKGARLRWLGEGALEVRPAESDDCGLDLLLSAGIHG 60 Query: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120 NETAPIELL+RLLH +A G ++PRAR+LFLFGNP AIRKGERF+EQD+NRLFNGRHE SS Sbjct: 61 NETAPIELLERLLHGVANGKIRPRARVLFLFGNPAAIRKGERFIEQDINRLFNGRHELSS 120 Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180 G EALRA ELE+ A FFS P R RLHYDLHTAIRGSKIEQFALYP+KE R+HSR+ELAR Sbjct: 121 GFEALRAAELEQFARVFFSKPGRNRLHYDLHTAIRGSKIEQFALYPYKEGRKHSRRELAR 180 Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240 L AAGMEAVLLQ+K SI FS++TY++L AEAFTLELGKARPFGQN+ VN+ LE+RL +I Sbjct: 181 LAAAGMEAVLLQSKSSITFSAFTYEQLEAEAFTLELGKARPFGQNEQVNLDKLEERLIRI 240 Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300 IE TEPE E +LDGLQL+SV+REIIKHSDSF L+LPADIENFSEL GYLLAED+A R Sbjct: 241 IEATEPE-DESSLDGLQLFSVSREIIKHSDSFHLHLPADIENFSELSKGYLLAEDLAEMR 299 Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENL 335 W++EEEGARIIFPNP+VKNGLRAGIL+VP + + L Sbjct: 300 WVVEEEGARIIFPNPKVKNGLRAGILIVPDSGQRL 334 Lambda K H 0.319 0.138 0.394 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: 435 Number of extensions: 18 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: 336 Length of database: 335 Length adjustment: 28 Effective length of query: 308 Effective length of database: 307 Effective search space: 94556 Effective search space used: 94556 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: 49 (23.5 bits)
Align candidate PP_4475 PP_4475 (succinylglutamate desuccinylase)
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.7137.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-135 435.5 0.0 7.1e-135 435.4 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4475 PP_4475 succinylglutamate desucc Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4475 PP_4475 succinylglutamate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.4 0.0 7.1e-135 7.1e-135 1 319 [] 6 327 .. 6 327 .. 0.97 Alignments for each domain: == domain 1 score: 435.4 bits; conditional E-value: 7.1e-135 TIGR03242 1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihGnetaPielleqllsdiaagk 72 ++l+ltl+++ep e+tq++ k+++lrwl+eG+le++P+ +++ +l++saGihGnetaPielle+ll+ +a+gk lcl|FitnessBrowser__Putida:PP_4475 6 KLLELTLTDHEPaEKTQVTPKGARLRWLGEGALEVRPAesDDCGLDLLLSAGIHGNETAPIELLERLLHGVANGK 80 589********98999999******************9888999******************************* PP TIGR03242 73 lqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasearyhyDlht 147 ++ ++r+L+++Gnpaa+rkg+R++e+d+nRlf+Gr+ el++++e+lRa+eLeq++++ff++++++ r+hyDlht lcl|FitnessBrowser__Putida:PP_4475 81 IRPRARVLFLFGNPAAIRKGERFIEQDINRLFNGRH-ELSSGFEALRAAELEQFARVFFSKPGRN--RLHYDLHT 152 ************************************.9**************************9..8******* PP TIGR03242 148 aiRasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendl 221 aiR+sk+e+fal+Py+ ++++++++l++laaa+++avll++++++tfs+f++e+leaea+tlelGkarPfG+n++ lcl|FitnessBrowser__Putida:PP_4475 153 AIRGSKIEQFALYPYKeGRKHSRRELARLAAAGMEAVLLQSKSSITFSAFTYEQLEAEAFTLELGKARPFGQNEQ 227 ****************99********************************************************* PP TIGR03242 222 sqfqaitealralisdeaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkde.ryr 293 +++++++e+l+++i ++++p+++++ l+lf+v ++i+k+sdsf+lh+++d++nf+e++kG+llaed +e r++ lcl|FitnessBrowser__Putida:PP_4475 228 VNLDKLEERLIRII-EATEPEDESSldGLQLFSVSREIIKHSDSFHLHLPADIENFSELSKGYLLAEDLAEmRWV 301 **************.7788887776679****************************************9988*** PP TIGR03242 294 veeeeerilfPnakvanGlRaglllv 319 veee++ri+fPn+kv+nGlRag+l+v lcl|FitnessBrowser__Putida:PP_4475 302 VEEEGARIIFPNPKVKNGLRAGILIV 327 ***********************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (319 nodes) Target sequences: 1 (335 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.00 // [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