Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_092482666.1 BM299_RS06535 lysine 2,3-aminomutase
Query= SwissProt::Q9XBQ8 (416 letters) >NCBI__GCF_900115975.1:WP_092482666.1 Length = 414 Score = 545 bits (1404), Expect = e-159 Identities = 251/399 (62%), Positives = 318/399 (79%) Query: 5 RYELFKDVSDADWNDWRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSLRMAITPYYL 64 R ++DV +DWNDWRWQ+RNRI +V++L++ + + EE +++C+K RMAITPYY Sbjct: 7 RVPYYQDVPASDWNDWRWQIRNRITSVDKLREVLGIQDEEAGEISRCLKHFRMAITPYYA 66 Query: 65 SLIDPNDPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDM 124 SLID ++ + P+++QA+PT ELN AD+ DPLHED DSPVPG+THRYPDRVLLL+TD Sbjct: 67 SLIDSSNKDCPIKRQAVPTIDELNFEEADMSDPLHEDVDSPVPGITHRYPDRVLLLVTDQ 126 Query: 125 CSMYCRHCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYI 184 CSMYCRHCTRRR AG D ++P ++D+AI YI+N +VRDVL+SGGD L +SDE LEYI Sbjct: 127 CSMYCRHCTRRRMAGGKDRALPRAQVDRAIAYIQNNKKVRDVLISGGDPLTLSDEHLEYI 186 Query: 185 IAKLREIPHVEIVRIGSRTPVVLPQRITPELVNMLKKYHPVWLNTHFNHPNEITEESTRA 244 I +LR + HVEI+RIG+RTPVVLPQRITPEL ML+KYHPVW+NTHFNHP EIT S + Sbjct: 187 IRRLRAVKHVEIIRIGTRTPVVLPQRITPELCAMLQKYHPVWINTHFNHPAEITLASKAS 246 Query: 245 CQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTP 304 C+ LADAG+PLGNQSVLLRG+NDC ++MK+L+++L+ +RVRPYY+YQCDLS G+ HFRT Sbjct: 247 CERLADAGIPLGNQSVLLRGINDCTNIMKKLLHQLMMMRVRPYYLYQCDLSRGIGHFRTS 306 Query: 305 VSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKTPVMPNYVISQSHDKVILRNFEGVITT 364 V KGIEI+E LRGHT+G VPT+VVDAPGGGGK PVMP Y IS+S +KVILRNFEG + + Sbjct: 307 VGKGIEIMENLRGHTTGLAVPTYVVDAPGGGGKIPVMPQYAISRSDNKVILRNFEGNVYS 366 Query: 365 YSEPINYTPGCNCDVCTGKKKVHKVGVAGLLNGEGMALE 403 Y+EP Y C+C+ C KK + G AGL+ G +ALE Sbjct: 367 YTEPAGYDADCHCEDCNNKKGKNSPGPAGLMKGNEVALE 405 Lambda K H 0.320 0.138 0.422 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: 582 Number of extensions: 15 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: 416 Length of database: 414 Length adjustment: 31 Effective length of query: 385 Effective length of database: 383 Effective search space: 147455 Effective search space used: 147455 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: 50 (23.9 bits)
Align candidate WP_092482666.1 BM299_RS06535 (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.291660.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-189 616.5 0.1 1.2e-189 616.2 0.1 1.0 1 NCBI__GCF_900115975.1:WP_092482666.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900115975.1:WP_092482666.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 616.2 0.1 1.2e-189 1.2e-189 4 380 .. 16 386 .. 13 399 .. 0.97 Alignments for each domain: == domain 1 score: 616.2 bits; conditional E-value: 1.2e-189 TIGR03820 4 eeewkdwkwqlrnsikdvdtlekllgiklseeekeelketvekfplsitpyylslidaedlendpiflqsvps 76 +++w+dw+wq+rn+i++vd+l+++lgi ++ee e+ + +++f ++itpyy+slid+++ + pi +q+vp+ NCBI__GCF_900115975.1:WP_092482666.1 16 ASDWNDWRWQIRNRITSVDKLREVLGI--QDEEAGEISRCLKHFRMAITPYYASLIDSSNKDC-PIKRQAVPT 85 689*********************998..588999*************************999.********* PP TIGR03820 77 skelevesadledplaedkdspvegithrypdrvlflvsntcamycrhctrkrkvgdkdsipskeeikegiey 149 ++el++e+ad++dpl+ed dspv+githrypdrvl+lv+++c+mycrhctr+r +g kd + + +++++i y NCBI__GCF_900115975.1:WP_092482666.1 86 IDELNFEEADMSDPLHEDVDSPVPGITHRYPDRVLLLVTDQCSMYCRHCTRRRMAGGKDRALPRAQVDRAIAY 158 ************************************************************************* PP TIGR03820 150 iretpqvrdvllsGGdplllsdelldwilselkaiehveviriGtrvpvvlpyritdelveilkkyhpvwlnt 222 i+++++vrdvl+sGGdpl lsde l++i+ l+a++hve+iriGtr+pvvlp+rit+el+++l+kyhpvw+nt NCBI__GCF_900115975.1:WP_092482666.1 159 IQNNKKVRDVLISGGDPLTLSDEHLEYIIRRLRAVKHVEIIRIGTRTPVVLPQRITPELCAMLQKYHPVWINT 231 ************************************************************************* PP TIGR03820 223 hfnhpkeitksskkalakladaGiplGnqsvllagvndcprilkklvhklvknrvrpyylyqcdlseGlshfr 295 hfnhp eit sk+++++ladaGiplGnqsvll+g+ndc++i+kkl h+l+ rvrpyylyqcdls+G+ hfr NCBI__GCF_900115975.1:WP_092482666.1 232 HFNHPAEITLASKASCERLADAGIPLGNQSVLLRGINDCTNIMKKLLHQLMMMRVRPYYLYQCDLSRGIGHFR 304 ************************************************************************* PP TIGR03820 296 tpvskGieilesliGhtsGfavptyvvdapgGGGkipvmpnylisqstnkvvlrnyeGvittykepdsyeeal 368 t+v+kGiei+e+l+Ght+G+avptyvvdapgGGGkipvmp+y is s+nkv+lrn+eG + +y+ep+ y++ NCBI__GCF_900115975.1:WP_092482666.1 305 TSVGKGIEIMENLRGHTTGLAVPTYVVDAPGGGGKIPVMPQYAISRSDNKVILRNFEGNVYSYTEPAGYDA-- 375 **********************************************************************9.. PP TIGR03820 369 cdrkcekcelkl 380 d +ce+c++k NCBI__GCF_900115975.1:WP_092482666.1 376 -DCHCEDCNNKK 386 .55677777654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (414 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: 21.48 // [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