Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate PfGW456L13_1977 Succinylglutamate desuccinylase (EC 3.5.1.96)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977 (336 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 Length = 336 Score = 662 bits (1707), Expect = 0.0 Identities = 336/336 (100%), Positives = 336/336 (100%) Query: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG Sbjct: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 Query: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS Sbjct: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120 Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR Sbjct: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180 Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI Sbjct: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240 Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR Sbjct: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300 Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA Sbjct: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 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: 521 Number of extensions: 13 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 PfGW456L13_1977 (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.11295.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-122 393.0 0.0 6.2e-122 392.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 Succinylglutamate desuccinylase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 Succinylglutamate desuccinylase (EC 3.5.1.96) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 392.8 0.0 6.2e-122 6.2e-122 1 319 [] 6 328 .. 6 328 .. 0.95 Alignments for each domain: == domain 1 score: 392.8 bits; conditional E-value: 6.2e-122 TIGR03242 1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihG 52 ++l+ltl+ +ep e+tq + ++v++rwl eG+le++P ++ +l++saGihG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 6 KLLELTLAGREPaEKTQLTVEGVRMRWLSEGALEVRPPeaRDNGLDLLLSAGIHG 60 589******9997889999*****************9855677889********* PP TIGR03242 53 netaPielleqllsdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGr 107 netaPiell++ll+dia+g+l+ ++r+L+++Gnp a+rkg+R++e+d+nRlf+Gr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGR 115 ******************************************************* PP TIGR03242 108 yqeleeskeklRaeeLeqvveaffeagkasearyhyDlhtaiRasklekfallPy 162 + e +++ e+lRa eLe ++ ff+ + ++ r+hyDlhtaiR+sk+e+fal+P lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 116 H-EQSSGCEALRACELERLAASFFSLPDRQ--RLHYDLHTAIRGSKIEQFALYPW 167 *.567888*******************998..8********************** PP TIGR03242 163 q.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPf 216 + ++++++++l++l+aa+++avll++++++ fs ++++kl+aea+tlelGkarPf lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 168 KeDRQHSRQELARLRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPF 222 999**************************************************** PP TIGR03242 217 Gendlsqfqaitealralisde..aiparkkeelklfevvesilkksdsfelhva 269 G+nd ++++ ++++l+++i ++ +++++ + l+l++v ++i+k+sdsf+l+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 223 GQNDGVNVSLLEKRLKQIIEGTepELTEDALDGLQLYSVAREIIKHSDSFRLNLP 277 *******************7651145566667*********************** PP TIGR03242 270 edasnftefakGtllaedkde.ryrveeeeerilfPnakvanGlRaglllv 319 +d++nf+e+++G+llaed ++ r+++eee++ri+fPn++v+nGlRag+l+v lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 278 ADIENFSELEVGYLLAEDIANtRWIIEEEGARIIFPNPRVKNGLRAGILVV 328 ******************8665***************************96 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.75 // [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