Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_014450628.1 LFE_RS12725 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000284315.1:WP_014450628.1 Length = 350 Score = 315 bits (808), Expect = 8e-91 Identities = 164/339 (48%), Positives = 236/339 (69%), Gaps = 13/339 (3%) Query: 5 LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEA-SPES 63 L V + GATGAVG++M+ LE+R F + L L +++RSAG KV+FKG+ +TV +PE Sbjct: 7 LCVGIFGATGAVGKEMISILEERRFPVGELRLFATERSAGEKVSFKGRTITVSSFDNPEK 66 Query: 64 FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEH-- 121 +G++IAL SAG + S ++P +G +VIDN+SAFRMD N PLVVPE+N + + + Sbjct: 67 AKGIHIALLSAGATPSLEISPILRDQGILVIDNSSAFRMDPNVPLVVPEINPSKIPAYPA 126 Query: 122 NGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKE 181 I+ANPNC+TIQM+ A++P+ G +++V+T+Q+VSG G +A+ EL +Q ILN Sbjct: 127 GAIVANPNCATIQMLLAIKPLIDCAGAKRIVVTTFQSVSGTGKDAMDELTTQLSLILNGR 186 Query: 182 --EIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAA 239 ++ P++ P +QIAFN +P ID F +GYT EE KM+NET+KI+ M D++V A Sbjct: 187 IGDVAPKVYP-------HQIAFNVLPHIDSFLPDGYTKEEEKMVNETRKILDMADIRVTA 239 Query: 240 TCVRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKN 299 T VR+P+ GHSE+V IE +RD + E + +L++APGV + D+PS YP+P D G++ Sbjct: 240 TTVRVPVMVGHSEAVNIEFERD-LSPETARKILEKAPGVKVLDNPSDCEYPLPMDVAGQD 298 Query: 300 DVFVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAE 338 DV+VGRIR+D +G +LWVV DNL KGAA N+VQIAE Sbjct: 299 DVYVGRIRRDFSVDHGLNLWVVGDNLRKGAALNAVQIAE 337 Lambda K H 0.314 0.131 0.366 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: 317 Number of extensions: 15 Number of successful extensions: 5 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: 346 Length of database: 350 Length adjustment: 29 Effective length of query: 317 Effective length of database: 321 Effective search space: 101757 Effective search space used: 101757 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 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_014450628.1 LFE_RS12725 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
# 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/TIGR01296.hmm # target sequence database: /tmp/gapView.3125345.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01296 [M=339] Accession: TIGR01296 Description: asd_B: aspartate-semialdehyde dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-134 434.4 0.0 1.7e-134 434.1 0.0 1.0 1 NCBI__GCF_000284315.1:WP_014450628.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014450628.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.1 0.0 1.7e-134 1.7e-134 2 334 .. 9 337 .. 8 340 .. 0.98 Alignments for each domain: == domain 1 score: 434.1 bits; conditional E-value: 1.7e-134 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaek.esfegidialfsaGgsv 73 v+i GatGavG+e++ +Leer fp+ +l+l+a ersaG+kv fkg+ ++v++ ++ e+ +gi ial saG++ NCBI__GCF_000284315.1:WP_014450628.1 9 VGIFGATGAVGKEMISILEERRFPVGELRLFATERSAGEKVSFKGRTITVSSFDNpEKAKGIHIALLSAGATP 81 89**************************************************86527999************* PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 s e+ p +g++viDn+safr+d++vPLvvpe+n +++ + i+anPnC+tiq++ ++kpl d a+ k NCBI__GCF_000284315.1:WP_014450628.1 82 SLEISPILRDQGILVIDNSSAFRMDPNVPLVVPEINPSKIPAYPAGAIVANPNCATIQMLLAIKPLIDCAGAK 154 ************************************************************************* PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 r+vv t+q+vsG+Gk++++eL+ q+ +l+g+ + + +k +++qiafn++p+id++ dGytkee+k+ NCBI__GCF_000284315.1:WP_014450628.1 155 RIVVTTFQSVSGTGKDAMDELTTQLSLILNGRIGD-----VAPKVYPHQIAFNVLPHIDSFLPDGYTKEEEKM 222 *****************************999888.....599****************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 ++etrkil++ d++v+at+vrvPv++ghse+v+iefe++ls+e ++++L++apgv+v+d+ps+ +yp P++++ NCBI__GCF_000284315.1:WP_014450628.1 223 VNETRKILDMADIRVTATTVRVPVMVGHSEAVNIEFERDLSPETARKILEKAPGVKVLDNPSDCEYPLPMDVA 295 ************************************************************************* PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiae 334 g+d+v+vgrir+D s ++gl+l+vv+DnlrkGaalnavqiae NCBI__GCF_000284315.1:WP_014450628.1 296 GQDDVYVGRIRRDFSVDHGLNLWVVGDNLRKGAALNAVQIAE 337 *****************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (350 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: 19.85 // [ok]
This GapMind analysis is from Jul 25 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