Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011867962.1 MMARC5_RS00960 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q57658 (354 letters) >NCBI__GCF_000016125.1:WP_011867962.1 Length = 348 Score = 515 bits (1326), Expect = e-151 Identities = 251/348 (72%), Positives = 294/348 (84%) Query: 7 MKIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENI 66 MKIKVG+LGATG+VGQRF+Q+L +HP+FEL AL AS+RSAGK Y+DACYW+Q IPE + Sbjct: 1 MKIKVGILGATGNVGQRFIQMLENHPVFELEALGASQRSAGKTYEDACYWYQTEAIPEEV 60 Query: 67 KDMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLV 126 V+ TDP + ++D+DIVFSALP+DLAK EPEFAK GK +FSNASA RME DVPL+ Sbjct: 61 ASATVVSTDPNDKAYDDIDIVFSALPADLAKTLEPEFAKRGKYVFSNASAMRMEADVPLI 120 Query: 127 IPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAV 186 IPEVN +H ++E+Q+ R DGAIITNPNCSTI AVI+LKPIMDKFG++ V I TMQA+ Sbjct: 121 IPEVNHEHFGMLEVQKSNRCSDGAIITNPNCSTIGAVISLKPIMDKFGIDLVNITTMQAI 180 Query: 187 SGAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAV 246 SGAGY+GVPSMAILDNL+P+I EEEKMQTE+LK+LG+++ + NFKI SCNRV V Sbjct: 181 SGAGYSGVPSMAILDNLVPYIGGEEEKMQTEALKILGSIEGNDFKNGNFKIGVSCNRVPV 240 Query: 247 IDGHTESIFVKTKEGAEPEEIKEVMDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNE 306 IDGHTESIFVKT E A PEEI +VMD FDPLK LNL +YAKPIV+REE DRPQPRLDRN Sbjct: 241 IDGHTESIFVKTTEEATPEEIAKVMDDFDPLKGLNLSSYAKPIVLREENDRPQPRLDRNT 300 Query: 307 GNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI 354 GNGMSIVVGR+RKDPIF+VKYTALEHNTIRGAAGASVLNAE FV+KY+ Sbjct: 301 GNGMSIVVGRVRKDPIFNVKYTALEHNTIRGAAGASVLNAELFVQKYL 348 Lambda K H 0.317 0.136 0.388 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: 451 Number of extensions: 12 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: 354 Length of database: 348 Length adjustment: 29 Effective length of query: 325 Effective length of database: 319 Effective search space: 103675 Effective search space used: 103675 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: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_011867962.1 MMARC5_RS00960 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR00978 (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/TIGR00978.hmm # target sequence database: /tmp/gapView.16000.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00978 [M=342] Accession: TIGR00978 Description: asd_EA: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-138 447.3 0.0 2e-138 447.1 0.0 1.0 1 lcl|NCBI__GCF_000016125.1:WP_011867962.1 MMARC5_RS00960 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_011867962.1 MMARC5_RS00960 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.1 0.0 2e-138 2e-138 1 341 [. 3 344 .. 3 345 .. 0.98 Alignments for each domain: == domain 1 score: 447.1 bits; conditional E-value: 2e-138 TIGR00978 1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepa 69 +kv++LGatG vGq+++++le+hp fel+++ as+r+aGk+y++++ w+ + ipeev ++++t+p+ lcl|NCBI__GCF_000016125.1:WP_011867962.1 3 IKVGILGATGNVGQRFIQMLENHPVFELEALGASQRSAGKTYEDACYWYQTEAIPEEVASATVVSTDPN 71 79******************************************************************9 PP TIGR00978 70 ae.ekdvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.g 136 + +d+d+vfsalp+++a+ +E+++a++G+ vfsnasa+R++ dvpli+pEvn +h+ +l+vqk lcl|NCBI__GCF_000016125.1:WP_011867962.1 72 DKaYDDIDIVFSALPADLAKTLEPEFAKRGKYVFSNASAMRMEADVPLIIPEVNHEHFGMLEVQKSNrC 140 76689************************************************************8769 PP TIGR00978 137 wkGvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekie 205 +G i+tnpnCst++ ++lkP++d+++i+ v ++t+qa+sGAGy+Gv+s++ildn++Pyi+gEEek++ lcl|NCBI__GCF_000016125.1:WP_011867962.1 141 SDGAIITNPNCSTIGAVISLKPIMDKFGIDLVNITTMQAISGAGYSGVPSMAILDNLVPYIGGEEEKMQ 209 9******************************************************************** PP TIGR00978 206 kEtkkilGkleegkvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglp 274 +E++kilG++e++ ++ ++++ ++++RvPv +GHtes+fv++ ++ +eei + +++f+ l + l+l lcl|NCBI__GCF_000016125.1:WP_011867962.1 210 TEALKILGSIEGNDFKNGNFKIGVSCNRVPVIDGHTESIFVKTTEEATPEEIAKVMDDFDPL-KGLNLS 277 *************************************************************9.99**** PP TIGR00978 275 saPekpivlldeedrPqprldldaekgmavtvGrlreese.slklvvlghnlvRGAAGaallnaElly 341 s+ kpivl++e+drPqprld+++++gm+++vGr+r++ ++k+ l hn++RGAAGa++lnaEl++ lcl|NCBI__GCF_000016125.1:WP_011867962.1 278 SY-AKPIVLREENDRPQPRLDRNTGNGMSIVVGRVRKDPIfNVKYTALEHNTIRGAAGASVLNAELFV 344 *9.9*************************************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (348 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.22 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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