Align Arginase; EC 3.5.3.1 (characterized)
to candidate WP_076582194.1 BB347_RS06745 arginase
Query= SwissProt::P39138 (296 letters) >NCBI__GCF_001971705.1:WP_076582194.1 Length = 306 Score = 288 bits (737), Expect = 1e-82 Identities = 153/308 (49%), Positives = 206/308 (66%), Gaps = 14/308 (4%) Query: 1 MDKTISVIGMPMDLGQARRGVDMGPSAIRYAHLIERLSDMGYTVEDLGDIPINREKIKN- 59 M +T+ ++G PMD G RRGVDMGPSAIRYA L +RL D G T D GD+ I R + ++ Sbjct: 1 MSETVRILGAPMDYGADRRGVDMGPSAIRYAGLADRLEDAGVTTIDDGDLSIPRAEERDP 60 Query: 60 ------DEELKNLNSVLAGNEKLAQKVNKVIEEKKFPLVLGGDHSIAIGTLAGTAKHYDN 113 D K L V +L ++V +E +FPLVLGGDHS+AIG++ G+A+ D Sbjct: 61 DAEQPADGHAKFLREVEDVCTRLGERVESALENGEFPLVLGGDHSVAIGSMRGSARDAD- 119 Query: 114 LGVIWYDAHGDLNTLETSPSGNIHGMPLAVSLGIGHESLVNLEGYAPKIKPENVVIIGAR 173 LG IW+DAH DLNT TSPSGN+HGMPLA +LG G V+ +AP+++ E++V +G R Sbjct: 120 LGAIWFDAHADLNTPATSPSGNVHGMPLAATLGRGAFGDVDW-AHAPRVREESIVYVGLR 178 Query: 174 SLDEGERKYIKESGMKVYTMHEIDRLGMTKVIEETLDY-LSACDGVHLSLDLDGLDPNDA 232 S+D+ ER+ ++ES M +TM +ID GMT V+E+ LD S DGVH+SLDLD LDP A Sbjct: 179 SIDDRERELVRESEMTAFTMADIDEYGMTAVVEDALDVATSGTDGVHVSLDLDWLDPKTA 238 Query: 233 PGVGTPVVGGISYRESHLAMEMLYD----AGIITSAEFVEVNPILDHKNKTGKTAVELVE 288 PGVGTPV GG++YRE+H A+E + G++ S + VEVNPILD +N+T + A EL Sbjct: 239 PGVGTPVRGGVTYREAHAALETVATRHGREGVVRSMDVVEVNPILDERNETARLAAELTA 298 Query: 289 SLLGKKLL 296 S G ++L Sbjct: 299 SAFGNRIL 306 Lambda K H 0.314 0.137 0.387 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: 14 Number of successful extensions: 6 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: 296 Length of database: 306 Length adjustment: 27 Effective length of query: 269 Effective length of database: 279 Effective search space: 75051 Effective search space used: 75051 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_076582194.1 BB347_RS06745 (arginase)
to HMM TIGR01229 (rocF: arginase (EC 3.5.3.1))
# 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/TIGR01229.hmm # target sequence database: /tmp/gapView.3448788.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01229 [M=300] Accession: TIGR01229 Description: rocF_arginase: arginase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-93 297.0 0.0 9.2e-93 296.8 0.0 1.0 1 NCBI__GCF_001971705.1:WP_076582194.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001971705.1:WP_076582194.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.8 0.0 9.2e-93 9.2e-93 2 298 .. 7 304 .. 6 306 .] 0.93 Alignments for each domain: == domain 1 score: 296.8 bits; conditional E-value: 9.2e-93 TIGR01229 2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesd.......reavkaersvla 67 i+g+p++ G+ +rGvd+Gp+a+r+agl+++l+d + + d+g+++ + + +e d + k++r v NCBI__GCF_001971705.1:WP_076582194.1 7 ILGAPMDYGADRRGVDMGPSAIRYAGLADRLEDAGVTTIDDGDLS-IPRAEERDpdaeqpaDGHAKFLREVED 78 89******************************************9.5555555557778887889******** PP TIGR01229 68 akeklaekvkkvveekrfplvLggdHsiaiGtvsgvakkakdkklgvlwlDAHaDintletstSgnlHGmPla 140 + +l e v+ e+++fplvLggdHs+aiG++ g a+ a d lg +w+DAHaD+nt+ ts+Sgn+HGmPla NCBI__GCF_001971705.1:WP_076582194.1 79 VCTRLGERVESALENGEFPLVLGGDHSVAIGSMRGSARDA-D--LGAIWFDAHADLNTPATSPSGNVHGMPLA 148 ***********************************99764.4..8**************************** PP TIGR01229 141 fllgrlkkevedleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklGiakvvektles 213 lgr ++ ++++ +++ + +++vy+GlR++d+ Er++++e+++++f+m +id++G+++vve +l+ NCBI__GCF_001971705.1:WP_076582194.1 149 ATLGRGAFG-----DVDWAHAPRVREESIVYVGLRSIDDRERELVRESEMTAFTMADIDEYGMTAVVEDALDV 216 ****54444.....467888889************************************************98 PP TIGR01229 214 lkaed.pihlSlDvDglDpklapatGtpvrgGltfrEgklilellle....sglltaldlvEvNPtldikeks 281 ++ + +h+SlD+D lDpk+ap++GtpvrgG+t+rE++ +le+++ +g + ++d+vEvNP+ld e++ NCBI__GCF_001971705.1:WP_076582194.1 217 ATSGTdGVHVSLDLDWLDPKTAPGVGTPVRGGVTYREAHAALETVATrhgrEGVVRSMDVVEVNPILD--ERN 287 765444***************************************98878899***************..*** PP TIGR01229 282 etikaavelvesllget 298 et++ a el++s++g+ NCBI__GCF_001971705.1:WP_076582194.1 288 ETARLAAELTASAFGNR 304 **************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (300 nodes) Target sequences: 1 (306 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: 25.11 // [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