Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_012968177.1 KVAR_RS12625 aspartate-semialdehyde dehydrogenase
Query= BRENDA::C5BB06 (367 letters) >NCBI__GCF_000025465.1:WP_012968177.1 Length = 372 Score = 418 bits (1075), Expect = e-121 Identities = 207/370 (55%), Positives = 267/370 (72%), Gaps = 4/370 (1%) Query: 1 MKNVGFIGWRGMVGSVLMQRMSEERDFDAIRPLFFSTSQHGQPAPTFGGHGGTLQDASDI 60 MK VG +GWRGMVGSVL+QRM EE DFD I FFSTS G P G L+DA+ + Sbjct: 1 MKQVGIVGWRGMVGSVLLQRMIEENDFDDISAHFFSTSSVGGVGPVINGKSDILKDANSL 60 Query: 61 DALKALDIIITCQGGDYTHAVYPRLRAAGWQGYWIDAASALRMQDDAIIILDPVNRAVID 120 AL +DIIITCQGGDYT A+YP L GWQGYWIDAASALRM + A IILDPVNR ID Sbjct: 61 SALAEMDIIITCQGGDYTKAIYPALINHGWQGYWIDAASALRMDEKACIILDPVNRDNID 120 Query: 121 RGLENGVKTFVGGNCTVSLMLMSLGGLFAADLVEWVSVATYQAASGGGARHMRELLTQMG 180 R ++ GVK FVGGNC+++L LM L GL ADL+EW+SV TYQ+ASG GA+ +REL+ Q Sbjct: 121 RAVKAGVKLFVGGNCSITLSLMGLAGLIKADLIEWMSVMTYQSASGAGAKQVRELIAQSA 180 Query: 181 MLHGQVAPALENPASAILDIERQVTDLMRNGTLPTDNFGVPLAGSLIPWIDKALDNGQSR 240 + ++ + ++L + +V++L+ + +P +NFGVPL GS+IPWID L +G SR Sbjct: 181 YISQHLSADELTASGSVLPLVNKVSELINSAGMPVENFGVPLMGSIIPWIDSDLGDGNSR 240 Query: 241 EEWKGQAETNKILA-SPQTIPIDGLCVRVGALRCHSQAFTVKLKRDIAIPEVEQLLARHN 299 EEWKG+AETNKIL +P TIP++GLC+RVG +RCHS A T+KLKR+++ E +L+ + Sbjct: 241 EEWKGEAETNKILGLAPGTIPVNGLCIRVGVIRCHSAAITLKLKREVSEAEFAELITHSH 300 Query: 300 EWVRVIPNDRELSMRELTPAAVTGTLATPVGRLRK--LNMGPQYLSAFTVGDQLLWGAAE 357 WV + N+++ S+ +LTPAA++G+L +GR +K LN P Y S TVGDQLLWGAAE Sbjct: 301 PWVNYVRNNKQESVNQLTPAAISGSLQVGIGRYKKMSLNNEPVY-SVLTVGDQLLWGAAE 359 Query: 358 PLRRMLRLLL 367 PLRRML +LL Sbjct: 360 PLRRMLNILL 369 Lambda K H 0.321 0.137 0.418 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: 403 Number of extensions: 13 Number of successful extensions: 3 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: 367 Length of database: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_012968177.1 KVAR_RS12625 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (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/TIGR01745.hmm # target sequence database: /tmp/gapView.626934.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01745 [M=366] Accession: TIGR01745 Description: asd_gamma: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-159 514.3 0.7 9.4e-159 514.1 0.7 1.0 1 NCBI__GCF_000025465.1:WP_012968177.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025465.1:WP_012968177.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 514.1 0.7 9.4e-159 9.4e-159 1 366 [] 2 369 .. 2 369 .. 0.98 Alignments for each domain: == domain 1 score: 514.1 bits; conditional E-value: 9.4e-159 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqg 73 k+vg+vgwrgmvgsvll+rm ee+dfd i++ ffsts +g+ +p++++ s il+da+ + al e+diiitcqg NCBI__GCF_000025465.1:WP_012968177.1 2 KQVGIVGWRGMVGSVLLQRMIEENDFDDISAHFFSTSSVGGVGPVINGKSDILKDANSLSALAEMDIIITCQG 74 68*********************************************************************** PP TIGR01745 74 gdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslggl 146 gdytk iyp l + gw+gywidaas+lrm++ a iildpvn d i+ av+ g++ fvggnc+++l lm+l gl NCBI__GCF_000025465.1:WP_012968177.1 75 GDYTKAIYPALINHGWQGYWIDAASALRMDEKACIILDPVNRDNIDRAVKAGVKLFVGGNCSITLSLMGLAGL 147 ************************************************************************* PP TIGR01745 147 frdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsv 219 ++ +l+ew+sv+tyq+asg+ga+ +rel+ q + +++ + +++s ++l + +kv++l+ s +pvenf+v NCBI__GCF_000025465.1:WP_012968177.1 148 IKADLIEWMSVMTYQSASGAGAKQVRELIAQSAYISQHLSADELTASGSVLPLVNKVSELINSAGMPVENFGV 220 ************************************************************************* PP TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilgtk.dtilvdglcvrigalrchsqaltiklkkdvsleeie 291 pl gs+ipwid +l +g+sreewkg+aetnkilg + ti+v+glc+r+g +rchs a+t+klk++vs e NCBI__GCF_000025465.1:WP_012968177.1 221 PLMGSIIPWIDSDLGDGNSREEWKGEAETNKILGLApGTIPVNGLCIRVGVIRCHSAAITLKLKREVSEAEFA 293 **********************************87379********************************** PP TIGR01745 292 eiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeyl.saftvgdqllwgaaeplrrmlr 363 e+i+ +wv++v n+++ ++++ltpaa++g+l++++gr +k+ + +e + s +tvgdqllwgaaeplrrml+ NCBI__GCF_000025465.1:WP_012968177.1 294 ELITHSHPWVNYVRNNKQESVNQLTPAAISGSLQVGIGRYKKMSLNNEPVySVLTVGDQLLWGAAEPLRRMLN 366 *******************************************99988553999******************* PP TIGR01745 364 ill 366 ill NCBI__GCF_000025465.1:WP_012968177.1 367 ILL 369 *96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (372 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: 18.44 // [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