Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate WP_066603038.1 V473_RS09535 N-carbamoylputrescine amidase
Query= SwissProt::Q9XGI9 (300 letters) >NCBI__GCF_001046645.1:WP_066603038.1 Length = 282 Score = 313 bits (802), Expect = 3e-90 Identities = 156/280 (55%), Positives = 190/280 (67%), Gaps = 8/280 (2%) Query: 8 VTVAALQFACTDDVSTNVATAERLVRAAHQKGANIILIQELFEGYYFCQAQKEEFFHRAK 67 VTVAALQ + +DD+ N+A VR A +GA IIL ELFEG YFC+ + E F A+ Sbjct: 4 VTVAALQLSFSDDMGENIAKVADHVRKAASRGAKIILPPELFEGPYFCRVEDEALFASAQ 63 Query: 68 PYPGHPTIVRMQNLAKELGVVIPVSFFEEANNAHYNSVAIIDADGTDLGLYRKSHIPDGP 127 P HP + M+ LAK+LGV IP SFFE + HYNS+A+ID G +G+YRKSHIPDGP Sbjct: 64 PIDTHPAVQEMRKLAKQLGVYIPTSFFERDGHHHYNSLAMIDDAGEIMGVYRKSHIPDGP 123 Query: 128 GYQEKYYFNPGDTGFKVFQTKYAKIGVAICWDQWFPEAARAMALQGAEVLFYPTAIGSEP 187 GY+EKYYF PG+TGFKV+ TKY IGV ICWDQW+PE AR MAL GAE+LFYPTAIGSEP Sbjct: 124 GYEEKYYFRPGNTGFKVWSTKYGTIGVGICWDQWYPETARCMALMGAEMLFYPTAIGSEP 183 Query: 188 QDDGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEITFYGYSFIAGPTGE 247 D LD+ WRR M GHA +N +P++A+NRIG E FYG+SFI G+ Sbjct: 184 YDSELDTSRMWRRAMIGHAVSNCMPVIAANRIGDE--------DGQLFYGHSFITDEWGD 235 Query: 248 LVAAAGDKEEAVLVAQFDLDKIKSKRHGWGVYRDRRPDLY 287 A A K++ LVA DL K + R G G +RDRRP+LY Sbjct: 236 FAAEADAKDQGALVATLDLAKARMHRAGMGFFRDRRPELY 275 Lambda K H 0.319 0.137 0.414 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: 302 Number of extensions: 10 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: 300 Length of database: 282 Length adjustment: 26 Effective length of query: 274 Effective length of database: 256 Effective search space: 70144 Effective search space used: 70144 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 WP_066603038.1 V473_RS09535 (N-carbamoylputrescine amidase)
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.1902163.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-139 448.8 0.0 4e-139 448.6 0.0 1.0 1 NCBI__GCF_001046645.1:WP_066603038.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046645.1:WP_066603038.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.6 0.0 4e-139 4e-139 1 279 [] 4 278 .. 4 278 .. 0.99 Alignments for each domain: == domain 1 score: 448.6 bits; conditional E-value: 4e-139 TIGR03381 1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplikrlqk 73 v+vaa+ql++s+d+ eni+k++++vr+aa++Ga+iil+pelfe+pyfc+ ++e+ f+ a+p++ hp++++++k NCBI__GCF_001046645.1:WP_066603038.1 4 VTVAALQLSFSDDMGENIAKVADHVRKAASRGAKIILPPELFEGPYFCRVEDEALFASAQPIDTHPAVQEMRK 76 79*********************************************************************** PP TIGR03381 74 lakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvwdtryakiG 146 lak+l+v +p+sffe++g+++ynsla+id Ge++gvyrkshiPdgpgyeek+yf+pG+tGfkvw t+y+ iG NCBI__GCF_001046645.1:WP_066603038.1 77 LAKQLGVYIPTSFFERDGHHHYNSLAMIDDAGEIMGVYRKSHIPDGPGYEEKYYFRPGNTGFKVWSTKYGTIG 149 ************************************************************************* PP TIGR03381 147 vgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvvaanrigkeveae 219 vgicWdqW+pe+ar++al+Gae+l+yPtaiGseP+d+eld++++W+ram Gha++n++pv+aanrig+e NCBI__GCF_001046645.1:WP_066603038.1 150 VGICWDQWYPETARCMALMGAEMLFYPTAIGSEPYDSELDTSRMWRRAMIGHAVSNCMPVIAANRIGDE---- 218 *********************************************************************.... PP TIGR03381 220 leltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpelyekl 279 + fyG+sfi+de+G+ aead ++++ lva++dl++++ +ra +G+frdrrpely ++ NCBI__GCF_001046645.1:WP_066603038.1 219 DGQLFYGHSFITDEWGDFAAEADAKDQGALVATLDLAKARMHRAGMGFFRDRRPELYGRI 278 6899*****************************************************875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (279 nodes) Target sequences: 1 (282 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: 12.04 // [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