Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_015944706.1 DHAF_RS18270 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000021925.1:WP_015944706.1 Length = 329 Score = 339 bits (869), Expect = 7e-98 Identities = 174/335 (51%), Positives = 238/335 (71%), Gaps = 9/335 (2%) Query: 6 HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE 65 +VA+VGATGAVGQ+ LK L +RNF ++ L LL++KRSAG K+ ++G+E+ VQE + +SF+ Sbjct: 3 NVAIVGATGAVGQEFLKILVERNFPVEELRLLATKRSAGKKILWQGREIEVQETTHDSFK 62 Query: 66 GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125 G++IALF AGGS S AP AVK GA+VIDN+SA+R+D PLVVPEVN D+ H GII Sbjct: 63 GIDIALF-AGGSSSTEFAPSAVKSGAVVIDNSSAYRLDPEVPLVVPEVNPEDVKWHKGII 121 Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEP 185 ANPNCSTI M AL+PI G+ +V+VSTYQAVSGAG E ++EL Q + + EE++ Sbjct: 122 ANPNCSTIIMAVALKPIFDLAGIKRVVVSTYQAVSGAGREGIEELEDQVRNWVQGEEVKS 181 Query: 186 EIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLP 245 + P YQIAFN IP+ID FQ+ YT EE KM+ ET+KI H+ + + AT VR+P Sbjct: 182 QTFP-------YQIAFNLIPRIDVFQEGDYTKEEWKMVKETQKIFHVDTMPITATTVRVP 234 Query: 246 IQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGR 305 + HSES+ IE +R ++++K ++APGV ++D+P++ YPMP ++V++GR Sbjct: 235 VLRSHSESINIETER-SVGLDEVKAAFQKAPGVIVEDNPAEDRYPMPWFTSDTDEVYIGR 293 Query: 306 IRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340 IRKD NG +LWVV D + KGAA N++QIAE L Sbjct: 294 IRKDFSIENGINLWVVGDQIRKGAATNTIQIAELL 328 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: 307 Number of extensions: 10 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 318 Effective length of database: 301 Effective search space: 95718 Effective search space used: 95718 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_015944706.1 DHAF_RS18270 (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.1275.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-144 466.0 0.1 3.9e-144 465.8 0.1 1.0 1 lcl|NCBI__GCF_000021925.1:WP_015944706.1 DHAF_RS18270 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_015944706.1 DHAF_RS18270 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.8 0.1 3.9e-144 3.9e-144 1 336 [. 3 328 .. 3 329 .] 0.99 Alignments for each domain: == domain 1 score: 465.8 bits; conditional E-value: 3.9e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nvaivGatGavGqe+lk+L ernfp+++l+lla +rsaGkk+ +g+e+ev+e+++ sf+gidialf a lcl|NCBI__GCF_000021925.1:WP_015944706.1 3 NVAIVGATGAVGQEFLKILVERNFPVEELRLLATKRSAGKKILWQGREIEVQETTHDSFKGIDIALF-A 70 79*****************************************************************.6 PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Ggs s efap+a+k+g++viDn+sa+rld++vPLvvpevn e++k +k giianPnCsti + v+Lkp lcl|NCBI__GCF_000021925.1:WP_015944706.1 71 GGSSSTEFAPSAVKSGAVVIDNSSAYRLDPEVPLVVPEVNPEDVKWHK--GIIANPNCSTIIMAVALKP 137 8888*****************************************998..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 + d a++krvvvstYqavsGaG++g+eeL++q++ +++g+e + +++f++qiafn+ip id + lcl|NCBI__GCF_000021925.1:WP_015944706.1 138 IFDLAGIKRVVVSTYQAVSGAGREGIEELEDQVRNWVQGEEVK-------SQTFPYQIAFNLIPRIDVF 199 ***************************************9987.......69***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e ytkee k++ et+ki++++ ++++at+vrvPv+++hses++ie+e+ + ++evk +++apgv+v lcl|NCBI__GCF_000021925.1:WP_015944706.1 200 QEGDYTKEEWKMVKETQKIFHVDTMPITATTVRVPVLRSHSESINIETERSVGLDEVKAAFQKAPGVIV 268 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336 d+p e+ yp+P ++++dev++grirkD s e+g++l+vv+D++rkGaa+n++qiaell lcl|NCBI__GCF_000021925.1:WP_015944706.1 269 EDNPAEDRYPMPWFTSDTDEVYIGRIRKDFSIENGINLWVVGDQIRKGAATNTIQIAELL 328 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (329 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: 00:00:00.01 # Mc/sec: 10.04 // [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