Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate WP_090447417.1 BLS63_RS19285 succinylglutamate desuccinylase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977 (336 letters) >NCBI__GCF_900100495.1:WP_090447417.1 Length = 336 Score = 520 bits (1340), Expect = e-152 Identities = 260/336 (77%), Positives = 293/336 (87%) Query: 1 MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60 MLALGKLLELTLAG EPA K QLT EG R+RWL+EGALEV P +A+DNGLDLLLSAGIHG Sbjct: 1 MLALGKLLELTLAGHEPAAKIQLTPEGARLRWLAEGALEVTPAQAQDNGLDLLLSAGIHG 60 Query: 61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120 NETAPIELLDRLL IARG+LKPR RILFLFGNP AIR+GERFVEQD+NRLFNGRHEQ + Sbjct: 61 NETAPIELLDRLLRGIARGELKPRTRILFLFGNPAAIRRGERFVEQDINRLFNGRHEQHT 120 Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180 G EA+RAC+LE LAA+FFS P R RLHYDLHTAIRGSKIEQFALYPW+E R S++ELAR Sbjct: 121 GFEAMRACDLEHLAATFFSKPGRTRLHYDLHTAIRGSKIEQFALYPWQEGRARSKRELAR 180 Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240 L AAG+EAVLL NK SI FS+YTY +LGAEAFTLELGKAR FGQN VN+ LLE+RL+ I Sbjct: 181 LNAAGIEAVLLHNKSSITFSAYTYTQLGAEAFTLELGKARAFGQNQQVNLELLEQRLQHI 240 Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300 IEG E E L+GLQL++VAREIIKHSD+F+++LPADIENFSEL VGYLLAED+A TR Sbjct: 241 IEGREAEQQSAELEGLQLFAVAREIIKHSDAFQMHLPADIENFSELPVGYLLAEDLAGTR 300 Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336 W++EE GARIIFPNP+VKNGLRAGIL+VP D +LA Sbjct: 301 WVVEESGARIIFPNPKVKNGLRAGILIVPADDSHLA 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: 418 Number of extensions: 19 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 WP_090447417.1 BLS63_RS19285 (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.10922.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-124 399.7 0.1 5.6e-124 399.5 0.1 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090447417.1 BLS63_RS19285 succinylglutamate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090447417.1 BLS63_RS19285 succinylglutamate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.5 0.1 5.6e-124 5.6e-124 1 319 [] 6 328 .. 6 328 .. 0.96 Alignments for each domain: == domain 1 score: 399.5 bits; conditional E-value: 5.6e-124 TIGR03242 1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihGnetaPielleqlls 66 ++l+ltl+ +ep + q + ++++lrwl+eG+le++P+ ++ +l++saGihGnetaPiell++ll+ lcl|NCBI__GCF_900100495.1:WP_090447417.1 6 KLLELTLAGHEPaAKIQLTPEGARLRWLAEGALEVTPAqaQDNGLDLLLSAGIHGNETAPIELLDRLLR 74 589*********6677888******************976677889*********************** PP TIGR03242 67 diaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagk 135 ia+g+l+ ++r+L+++Gnpaa+r+g+R++e+d+nRlf+Gr+ e ++++e++Ra +Le+ +++ff++++ lcl|NCBI__GCF_900100495.1:WP_090447417.1 75 GIARGELKPRTRILFLFGNPAAIRRGERFVEQDINRLFNGRH-EQHTGFEAMRACDLEHLAATFFSKPG 142 ******************************************.6688********************** PP TIGR03242 136 asearyhyDlhtaiRasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfsseklea 203 ++ r+hyDlhtaiR+sk+e+fal+P q ++ +k++l++l+aa+++avllh+++++tfs++++ +l+a lcl|NCBI__GCF_900100495.1:WP_090447417.1 143 RT--RLHYDLHTAIRGSKIEQFALYPWQeGRARSKRELARLNAAGIEAVLLHNKSSITFSAYTYTQLGA 209 *9..8**********************999*************************************** PP TIGR03242 204 eactlelGkarPfGendlsqfqaitealralisdeaiparkke..elklfevvesilkksdsfelhvae 270 ea+tlelGkar fG+n++++++ ++++l+ +i +++ ++++e l+lf v ++i+k+sd+f++h+++ lcl|NCBI__GCF_900100495.1:WP_090447417.1 210 EAFTLELGKARAFGQNQQVNLELLEQRLQHIIEGREAEQQSAEleGLQLFAVAREIIKHSDAFQMHLPA 278 ********************************98888777776779*********************** PP TIGR03242 271 dasnftefakGtllaedkde.ryrveeeeerilfPnakvanGlRaglllv 319 d++nf+e+++G+llaed + r++vee+++ri+fPn+kv+nGlRag+l+v lcl|NCBI__GCF_900100495.1:WP_090447417.1 279 DIENFSELPVGYLLAEDLAGtRWVVEESGARIIFPNPKVKNGLRAGILIV 328 *****************9866**************************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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.71 // [ok]
This GapMind analysis is from Sep 24 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