Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate WP_012502633.1 CPAR_RS07105 lysine 2,3-aminomutase
Query= BRENDA::G3F9X2 (437 letters) >NCBI__GCF_000020505.1:WP_012502633.1 Length = 440 Score = 639 bits (1647), Expect = 0.0 Identities = 296/431 (68%), Positives = 351/431 (81%) Query: 7 AQKEIAKKIDSDTVIANWKDWRWQLKHSIGDIDTFETLLGIKFKPGEKDKLKQTLEKFPL 66 AQK+I K+ID +T ++W DWRWQ++HSI D+DTFE LL I ++ +T++KFP+ Sbjct: 6 AQKQIIKRIDPETTPSDWSDWRWQMRHSIRDLDTFERLLDITLSDEQRKAFGETVQKFPM 65 Query: 67 SVTPYYLSLIDAEDFRNDPIFLQAFPSPKELDIDEDDLEDPLSEDEDSPVEGITHRYPDR 126 S TPYYLSLI+ +D NDP+FLQ+ PSP EL I + D+ DPL EDEDSP +THRYPDR Sbjct: 66 STTPYYLSLINTDDMENDPVFLQSVPSPLELKIMKGDMADPLHEDEDSPAPCVTHRYPDR 125 Query: 127 VLFHISNTCSMYCRHCTRKRKVGDVDSIPTKDAVSEGLEYIRNTPQVRDVLLSGGDPFML 186 VL +SNTC MYCRHCTRKRKVGD D+IP + A+ G++YIRNTPQVRDVLLSGGDPF+L Sbjct: 126 VLLLVSNTCPMYCRHCTRKRKVGDEDTIPNRAAIQAGIDYIRNTPQVRDVLLSGGDPFLL 185 Query: 187 PDAYLDWILAKLREIPHVEIIRIGTRMPVVLPYRVTDDLVKILKKHHPLWINTHFNHPRE 246 D LDWIL +LR I HVEIIR+GTR PVVLP R+T +LV IL KH P+W+NTHFNHPRE Sbjct: 186 SDEMLDWILTELRAIEHVEIIRVGTRTPVVLPQRITPELVAILGKHQPVWVNTHFNHPRE 245 Query: 247 VTASSREALRKLADAGIPLGNQTVLLSGVNDCHRIMKRLVQKLVQNRVRPYYLYQCDLSE 306 +T S+R AL +LAD G+PLGNQTVLLSG+NDC RIMK LV KLV NRVRPYYLYQCDLSE Sbjct: 246 MTQSARNALARLADVGVPLGNQTVLLSGINDCPRIMKALVHKLVANRVRPYYLYQCDLSE 305 Query: 307 GLSHFRTPVGKGIEIMEHLIGHTSGFAVPTYVIDAPHGGGKIPVMPSYLISWSTNRVILR 366 GLSHFRTPVGKGIEI+E LIGHTSGF VPTYVIDAP GGGKIPVMP+YLISWSTN+V+LR Sbjct: 306 GLSHFRTPVGKGIEILESLIGHTSGFCVPTYVIDAPGGGGKIPVMPNYLISWSTNKVVLR 365 Query: 367 NYEGVITSYKEPDSYEPIYCDRKCEECKLQLKLDDAAEYKSTGIAKLLADNDEVVSLVPE 426 NYEGVIT+YKEPDSYEP +CDR C EC LQL +DA + K+ G+ +LLAD+D+ +SL+P Sbjct: 366 NYEGVITTYKEPDSYEPTFCDRNCTECDLQLNFEDAEQSKAIGVQQLLADHDQTISLIPS 425 Query: 427 DTERMERRDVE 437 R +RR E Sbjct: 426 SNARHKRRKGE 436 Lambda K H 0.319 0.138 0.420 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: 651 Number of extensions: 21 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: 437 Length of database: 440 Length adjustment: 32 Effective length of query: 405 Effective length of database: 408 Effective search space: 165240 Effective search space used: 165240 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: 51 (24.3 bits)
Align candidate WP_012502633.1 CPAR_RS07105 (lysine 2,3-aminomutase)
to HMM TIGR03820 (ablA: lysine-2,3-aminomutase (EC 5.4.3.2))
# 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/TIGR03820.hmm # target sequence database: /tmp/gapView.453952.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03820 [M=417] Accession: TIGR03820 Description: lys_2_3_AblA: lysine-2,3-aminomutase 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-239 779.4 0.0 4.2e-239 779.2 0.0 1.0 1 NCBI__GCF_000020505.1:WP_012502633.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000020505.1:WP_012502633.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 779.2 0.0 4.2e-239 4.2e-239 3 417 .] 19 433 .. 17 433 .. 0.99 Alignments for each domain: == domain 1 score: 779.2 bits; conditional E-value: 4.2e-239 TIGR03820 3 seeewkdwkwqlrnsikdvdtlekllgiklseeekeelketvekfplsitpyylslidaedlendpiflqsvp 75 + ++w+dw+wq+r+si+d+dt+e+ll+i+ls+e+++++ etv+kfp+s tpyylsli+++d+endp+flqsvp NCBI__GCF_000020505.1:WP_012502633.1 19 TPSDWSDWRWQMRHSIRDLDTFERLLDITLSDEQRKAFGETVQKFPMSTTPYYLSLINTDDMENDPVFLQSVP 91 5689********************************************************************* PP TIGR03820 76 sskelevesadledplaedkdspvegithrypdrvlflvsntcamycrhctrkrkvgdkdsipskeeikegie 148 s+ el++++ d++dpl+ed+dsp++++thrypdrvl+lvsntc mycrhctrkrkvgd+d+ip++ i++gi+ NCBI__GCF_000020505.1:WP_012502633.1 92 SPLELKIMKGDMADPLHEDEDSPAPCVTHRYPDRVLLLVSNTCPMYCRHCTRKRKVGDEDTIPNRAAIQAGID 164 ************************************************************************* PP TIGR03820 149 yiretpqvrdvllsGGdplllsdelldwilselkaiehveviriGtrvpvvlpyritdelveilkkyhpvwln 221 yir+tpqvrdvllsGGdp+llsde+ldwil+el+aiehve+ir+Gtr+pvvlp+rit+elv+il k++pvw+n NCBI__GCF_000020505.1:WP_012502633.1 165 YIRNTPQVRDVLLSGGDPFLLSDEMLDWILTELRAIEHVEIIRVGTRTPVVLPQRITPELVAILGKHQPVWVN 237 ************************************************************************* PP TIGR03820 222 thfnhpkeitksskkalakladaGiplGnqsvllagvndcprilkklvhklvknrvrpyylyqcdlseGlshf 294 thfnhp+e+t+s+++ala+lad+G+plGnq+vll+g+ndcpri+k+lvhklv+nrvrpyylyqcdlseGlshf NCBI__GCF_000020505.1:WP_012502633.1 238 THFNHPREMTQSARNALARLADVGVPLGNQTVLLSGINDCPRIMKALVHKLVANRVRPYYLYQCDLSEGLSHF 310 ************************************************************************* PP TIGR03820 295 rtpvskGieilesliGhtsGfavptyvvdapgGGGkipvmpnylisqstnkvvlrnyeGvittykepdsyeea 367 rtpv+kGieilesliGhtsGf+vptyv+dapgGGGkipvmpnylis+stnkvvlrnyeGvittykepdsye++ NCBI__GCF_000020505.1:WP_012502633.1 311 RTPVGKGIEILESLIGHTSGFCVPTYVIDAPGGGGKIPVMPNYLISWSTNKVVLRNYEGVITTYKEPDSYEPT 383 ************************************************************************* PP TIGR03820 368 lcdrkcekcelklkledaeeskavGieklladeddtislvpeenerlerr 417 +cdr+c++c+l+l+ edae+ska+G+++llad+d+tisl+p++n r++rr NCBI__GCF_000020505.1:WP_012502633.1 384 FCDRNCTECDLQLNFEDAEQSKAIGVQQLLADHDQTISLIPSSNARHKRR 433 ***********************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (440 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 25.39 // [ok]
This GapMind analysis is from Apr 09 2024. 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