Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_106716171.1 CU100_RS08500 cysteine synthase A
Query= BRENDA::C4ITG6 (334 letters) >NCBI__GCF_003010935.1:WP_106716171.1 Length = 324 Score = 503 bits (1294), Expect = e-147 Identities = 252/325 (77%), Positives = 287/325 (88%), Gaps = 6/325 (1%) Query: 14 LGSKDAEAAGRGRIYDSILDTIGNTPLVRIDKFARENGVKANLLVKLEFFNPLASVKDRI 73 + S+ GRGRIY+SI+DTIG+TPL+R+DK A+E GV ANLL KLEFFNP++SVKDRI Sbjct: 1 MSSESVRKPGRGRIYNSIVDTIGDTPLIRLDKLAKEKGVGANLLAKLEFFNPISSVKDRI 60 Query: 74 GLAMIEALEKQGKAVPGKTVFVEPTSGNTGIALAFAAAAKGYRLILTMPETMSMERRKLL 133 G+A+IEALE QG+A PGKT +EPTSGNTGIALAFAAAAKGYRLILTMPETMS+ERRK+L Sbjct: 61 GVALIEALEVQGRATPGKTTLIEPTSGNTGIALAFAAAAKGYRLILTMPETMSVERRKML 120 Query: 134 RLLGAELVLTEGAKGMKGAIAEA----EAIGNPNAIIPQQFENPANPEIHRLTTAEEIWN 189 +LLGAELVLTEGAKGMKGAIA+A E IG+ A+IP QF+NPANPEIHR TTAEEIWN Sbjct: 121 KLLGAELVLTEGAKGMKGAIAKANELVETIGD--AVIPGQFDNPANPEIHRRTTAEEIWN 178 Query: 190 DTNGEADILISGIGTGGTITGVGQVIKARKPSFKVVAVEPKDSPVLSGGAPGPHKIQGLG 249 DT G DIL++GIGTGGTITGVGQV+K RKP VVAVEPKDSP+LSGG PGPHKIQG+G Sbjct: 179 DTEGSVDILVAGIGTGGTITGVGQVLKQRKPGVLVVAVEPKDSPILSGGNPGPHKIQGIG 238 Query: 250 AGFAPKTLDTGIYDEIVQISNEDAFTNARLVARLEGIPVGISSGAALAAAIEVGKRSENA 309 AGFAP LDT IYDE+VQ+SNED+F NARLVAR+EG+PVGISSGAAL AAIEVG+R EN Sbjct: 239 AGFAPAVLDTHIYDEVVQVSNEDSFANARLVARIEGVPVGISSGAALTAAIEVGQRPENK 298 Query: 310 GKNIVVVIPSFAERYLSTALFEGLE 334 GKN+VV+IPSFAERYLSTALFEGL+ Sbjct: 299 GKNLVVIIPSFAERYLSTALFEGLD 323 Lambda K H 0.314 0.134 0.373 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: 417 Number of extensions: 6 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: 334 Length of database: 324 Length adjustment: 28 Effective length of query: 306 Effective length of database: 296 Effective search space: 90576 Effective search space used: 90576 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: 49 (23.5 bits)
Align candidate WP_106716171.1 CU100_RS08500 (cysteine synthase A)
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))
# 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.aa/TIGR01139.hmm # target sequence database: /tmp/gapView.3199456.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01139 [M=298] Accession: TIGR01139 Description: cysK: cysteine synthase A 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-135 434.8 1.3 9.2e-135 434.6 1.3 1.0 1 NCBI__GCF_003010935.1:WP_106716171.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106716171.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.6 1.3 9.2e-135 9.2e-135 2 298 .] 19 319 .. 18 319 .. 0.98 Alignments for each domain: == domain 1 score: 434.6 bits; conditional E-value: 9.2e-135 TIGR01139 2 seliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveatsGntGi 70 ++iG+tPl+rL+ ++++ a++l+kle++nP ssvkdri++a+ie e +g ++gk t++e+tsGntGi NCBI__GCF_003010935.1:WP_106716171.1 19 VDTIGDTPLIRLDklaKEKGVGANLLAKLEFFNPISSVKDRIGVALIEALEVQGRATPGKtTLIEPTSGNTGI 91 589*********98544567789************************************989*********** PP TIGR01139 71 alamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpa 143 ala+ aaa+gy+liltmpetms+errk+lk +GaelvLt+ga+gmkgai+ka+elve+ +++ ++ qf+npa NCBI__GCF_003010935.1:WP_106716171.1 92 ALAFAAAAKGYRLILTMPETMSVERRKMLKLLGAELVLTEGAKGMKGAIAKANELVETIGDAV-IPGQFDNPA 163 ************************************************************776.********* PP TIGR01139 144 npeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqG 216 npeihr+tta+ei++d++g++d++vag+GtGGtitGvg+vlk+ kp + vvaveP++sp+lsgg+pgphkiqG NCBI__GCF_003010935.1:WP_106716171.1 164 NPEIHRRTTAEEIWNDTEGSVDILVAGIGTGGTITGVGQVLKQRKPGVLVVAVEPKDSPILSGGNPGPHKIQG 236 ************************************************************************* PP TIGR01139 217 igagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdt 288 igagf P+vLd++++dev++vs+e++++ ar +a+ eG+ vGissGaa+ aa++v +++e k+k++vvi+p++ NCBI__GCF_003010935.1:WP_106716171.1 237 IGAGFAPAVLDTHIYDEVVQVSNEDSFANARLVARIEGVPVGISSGAALTAAIEVGQRPEnKGKNLVVIIPSF 309 ***********************************************************99************ PP TIGR01139 289 gerYlstaLf 298 +erYlstaLf NCBI__GCF_003010935.1:WP_106716171.1 310 AERYLSTALF 319 *********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (324 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 16.67 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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