Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate Pf1N1B4_3447 Succinylglutamate desuccinylase (EC 3.5.1.96)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977 (336 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 Length = 336 Score = 625 bits (1612), Expect = 0.0 Identities = 312/336 (92%), Positives = 327/336 (97%) Query: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG Sbjct: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 Query: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIR+GERF+EQDVNRLFNGRHEQ+S Sbjct: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRRGERFIEQDVNRLFNGRHEQTS 120 Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180 G EALRACELERLAA+FFSLPDR RLHYDLHTAIRGSKIEQFALYPWKE RQHSR ELAR Sbjct: 121 GSEALRACELERLAATFFSLPDRNRLHYDLHTAIRGSKIEQFALYPWKEGRQHSRLELAR 180 Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240 LRAAGMEAVLLQNKPSIVFSSYTYDKL AE+FTLELGKARPFGQNDGVNVSLLE RLKQI Sbjct: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLDAESFTLELGKARPFGQNDGVNVSLLETRLKQI 240 Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300 IEGTEP +T+D LDGLQL+SVARE+IKHSDSFRLNLP DIENFSEL+VGY+LAEDIANTR Sbjct: 241 IEGTEPPMTDDGLDGLQLFSVAREVIKHSDSFRLNLPTDIENFSELKVGYVLAEDIANTR 300 Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336 W+IEE+GARIIFPNP+VKNGLRAGIL+VPTTDENLA Sbjct: 301 WVIEEKGARIIFPNPKVKNGLRAGILIVPTTDENLA 336 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: 515 Number of extensions: 18 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: 336 Length of database: 336 Length adjustment: 28 Effective length of query: 308 Effective length of database: 308 Effective search space: 94864 Effective search space used: 94864 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 Pf1N1B4_3447 (Succinylglutamate desuccinylase (EC 3.5.1.96))
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.28271.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-121 389.3 0.0 8.4e-121 389.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 Succinylglutamate desuccinylase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 Succinylglutamate desuccinylase (EC 3.5.1.96) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.1 0.0 8.4e-121 8.4e-121 1 319 [] 6 328 .. 6 328 .. 0.95 Alignments for each domain: == domain 1 score: 389.1 bits; conditional E-value: 8.4e-121 TIGR03242 1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihGnetaPiell 61 ++l+ltl+ +ep e+tq + ++v++rwl eG+le++P ++ +l++saGihGnetaPiell lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 6 KLLELTLAGREPaEKTQLTVEGVRMRWLSEGALEVRPPeaRDNGLDLLLSAGIHGNETAPIELL 69 589******9997889999*****************9855677889****************** PP TIGR03242 62 eqllsdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeq 125 ++ll+dia+g+l+ ++r+L+++Gnp a+r+g+R++e+d+nRlf+Gr+ e +++ e+lRa eLe lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 70 DRLLHDIARGDLKPRARILFLFGNPEAIRRGERFIEQDVNRLFNGRH-EQTSGSEALRACELER 132 ***********************************************.567899********** PP TIGR03242 126 vveaffeagkasearyhyDlhtaiRasklekfallPyq.ekpfdkellewlaaadldavllhke 188 +++ff+ + ++ r+hyDlhtaiR+sk+e+fal+P + ++++++ +l++l+aa+++avll+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 133 LAATFFSLPDRN--RLHYDLHTAIRGSKIEQFALYPWKeGRQHSRLELARLRAAGMEAVLLQNK 194 **********99..8**********************999************************ PP TIGR03242 189 kggtfshfssekleaeactlelGkarPfGendlsqfqaitealralisdeaiparkke..elkl 250 +++ fs ++++kl+ae++tlelGkarPfG+nd ++++ ++++l+++i +++ p++ l+l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 195 PSIVFSSYTYDKLDAESFTLELGKARPFGQNDGVNVSLLETRLKQIIEGTEPPMTDDGldGLQL 258 ***********************************************88877765543559*** PP TIGR03242 251 fevvesilkksdsfelhvaedasnftefakGtllaedkde.ryrveeeeerilfPnakvanGlR 313 f+v ++++k+sdsf+l+++ d++nf+e+++G++laed ++ r+++ee+++ri+fPn+kv+nGlR lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 259 FSVAREVIKHSDSFRLNLPTDIENFSELKVGYVLAEDIANtRWVIEEKGARIIFPNPKVKNGLR 322 *************************************8665*********************** PP TIGR03242 314 aglllv 319 ag+l+v lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3447 323 AGILIV 328 ***996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (319 nodes) Target sequences: 1 (336 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: 11.85 // [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