Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate Pf1N1B4_4326 N-carbamoylputrescine amidase (3.5.1.53)
Query= SwissProt::Q8VYF5 (299 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 Length = 302 Score = 329 bits (844), Expect = 4e-95 Identities = 155/288 (53%), Positives = 208/288 (72%), Gaps = 1/288 (0%) Query: 10 VVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKRAK 69 + +++ Q C+ D+ N+ AERLVREA AKGA +IL+QELF YFC Q A+ Sbjct: 4 LTIATTQMPCTWDLQHNLDQAERLVREAAAKGAQVILLQELFATPYFCIEQSHKHLALAE 63 Query: 70 PYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPDGP 129 Y++ P + R LAKELGVV+P+S+FE+A A++NS+++ DADG LG+YRK+HIP+ Sbjct: 64 EYRDSPVLKRFAALAKELGVVLPLSWFEKAGNAYFNSLSVADADGRLLGVYRKTHIPNAI 123 Query: 130 GYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGSEP 189 GYQEK YF+PGDTGF+V+ T F +IGV ICWDQWFPE AR + L GAE+L +PTAIGSEP Sbjct: 124 GYQEKEYFSPGDTGFRVWDTAFGRIGVGICWDQWFPETARCLALMGAEVLLFPTAIGSEP 183 Query: 190 QDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPTGE 249 LDSRDHW+ M+GHA AN++P+VA+NR+G E+ T+ Q+ FYG+SFI G+ Sbjct: 184 GCAALDSRDHWQMTMRGHAAANILPVVAANRVGPEVATTD-PTLQMNFYGSSFICNHKGK 242 Query: 250 IVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDG 297 ++AEAD S VLV DL ++ +R SWG++RDRRPD+Y LL+ DG Sbjct: 243 LLAEADRDSTGVLVHSLDLTAMREERLSWGIYRDRRPDMYGALLSQDG 290 Lambda K H 0.321 0.137 0.410 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: 287 Number of extensions: 7 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: 299 Length of database: 302 Length adjustment: 27 Effective length of query: 272 Effective length of database: 275 Effective search space: 74800 Effective search space used: 74800 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate Pf1N1B4_4326 (N-carbamoylputrescine amidase (3.5.1.53))
to HMM TIGR03381 (aguB: N-carbamoylputrescine amidase (EC 3.5.1.53))
# 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/TIGR03381.hmm # target sequence database: /tmp/gapView.8986.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03381 [M=279] Accession: TIGR03381 Description: agmatine_aguB: N-carbamoylputrescine amidase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-141 454.7 0.0 6.5e-141 454.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 N-carbamoylputrescine amidase (3 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 N-carbamoylputrescine amidase (3.5.1.53) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 454.5 0.0 6.5e-141 6.5e-141 2 278 .. 5 284 .. 4 285 .. 0.98 Alignments for each domain: == domain 1 score: 454.5 bits; conditional E-value: 6.5e-141 TIGR03381 2 kvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveeh 65 ++a++q+ +++d+++n+++ae+lvreaaakGaq+ill+elf++pyfc eq++++++la++++++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 5 TIATTQMPCTWDLQHNLDQAERLVREAAAKGAQVILLQELFATPYFCIEQSHKHLALAEEYRDS 68 89************************************************************** PP TIGR03381 66 plikrlqklakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfk 129 p++kr+++lakel+vvlp+s+fekagna++nsl v+dadG+ lgvyrk+hiP+++gy+ek yf+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 69 PVLKRFAALAKELGVVLPLSWFEKAGNAYFNSLSVADADGRLLGVYRKTHIPNAIGYQEKEYFS 132 **************************************************************** PP TIGR03381 130 pGdtGfkvwdtryakiGvgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqr 193 pGdtGf+vwdt++++iGvgicWdqWfpe+ar+lal+Gaevll+PtaiGseP a+lds++hWq lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 133 PGDTGFRVWDTAFGRIGVGICWDQWFPETARCLALMGAEVLLFPTAIGSEPGCAALDSRDHWQM 196 **************************************************************** PP TIGR03381 194 amqGhaaanvvpvvaanrigkeveae...leltfyGssfiadetGelvaeadrseeavlvaefd 254 +m+Ghaaan++pvvaanr+g ev+++ l+++fyGssfi++++G+l+aeadr+ ++vlv+++d lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 197 TMRGHAAANILPVVAANRVGPEVATTdptLQMNFYGSSFICNHKGKLLAEADRDSTGVLVHSLD 260 **********************87766669********************************** PP TIGR03381 255 ldeiakeraawGlfrdrrpelyek 278 l ++++er +wG++rdrrp++y + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 261 LTAMREERLSWGIYRDRRPDMYGA 284 **********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (279 nodes) Target sequences: 1 (302 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: 9.42 // [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