Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate CA265_RS15395 CA265_RS15395 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >FitnessBrowser__Pedo557:CA265_RS15395 Length = 329 Score = 295 bits (754), Expect = 1e-84 Identities = 160/342 (46%), Positives = 224/342 (65%), Gaps = 13/342 (3%) Query: 5 LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64 + VAVVGATG VG MLK LE+RNF + L ++S++S G ++TFKG++ + Sbjct: 1 MKVAVVGATGLVGTVMLKVLEERNFPLTELIPVASEKSVGKEITFKGKKFPIVSMDTAIS 60 Query: 65 EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124 +IALFSAGG+ S AP + G VIDN+SA+RMD L+VPEVN +L N I Sbjct: 61 MKPDIALFSAGGNTSLEHAPRFKEAGTTVIDNSSAWRMDPAIKLIVPEVNAHELSIDNKI 120 Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184 IANPNCSTIQMV L+P+ Y + +V+VSTYQ+V+G G +AV++L ++ + + Sbjct: 121 IANPNCSTIQMVVVLKPLHDKYKIKRVVVSTYQSVTGTGVKAVEQLMNERKGVDG----- 175 Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244 P+ P Y+I N +P ID F +NGYT EEMKM+ ET KIM ++V AT VR+ Sbjct: 176 PKAYP-------YEIDLNVLPHIDVFMENGYTKEEMKMVKETNKIMSDDSIKVTATTVRI 228 Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304 P+ GHSESV IE + +D + +++++L+++PG+ + DD + YPMP DA K++VFVG Sbjct: 229 PVMGGHSESVNIEFE-NDFDLAEVRSILEKSPGIIVVDDVANLKYPMPKDAHEKDEVFVG 287 Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 RIR+D +LW+V+DNL KGAA N+VQIAE L + LV Sbjct: 288 RIRRDESAPKALNLWIVADNLRKGAATNAVQIAEYLIQKELV 329 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: 285 Number of extensions: 8 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: 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 CA265_RS15395 CA265_RS15395 (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.5511.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-135 436.9 3.2 4.8e-135 436.0 3.2 1.4 1 lcl|FitnessBrowser__Pedo557:CA265_RS15395 CA265_RS15395 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS15395 CA265_RS15395 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.0 3.2 4.8e-135 4.8e-135 1 338 [. 2 325 .. 2 326 .. 0.98 Alignments for each domain: == domain 1 score: 436.0 bits; conditional E-value: 4.8e-135 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfs 68 +va+vGatG vG ++lkvLeernfp+ +l+++ase+s Gk+++fkgk++ + +++++ + dialfs lcl|FitnessBrowser__Pedo557:CA265_RS15395 2 KVAVVGATGLVGTVMLKVLEERNFPLTELIPVASEKSVGKEITFKGKKFPIVSMDTAISMKPDIALFS 69 69*******************************************************999******** PP TIGR01296 69 aGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvL 136 aGg++s e ap++ +ag++viDn+sa+r+d+ + L+vpevna+el + iianPnCstiq+vvvL lcl|FitnessBrowser__Pedo557:CA265_RS15395 70 AGGNTSLEHAPRFKEAGTTVIDNSSAWRMDPAIKLIVPEVNAHELSIDN--KIIANPNCSTIQMVVVL 135 *********************************************9988..8**************** PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaipli 204 kpl+d++k+krvvvstYq+v G+G k+ve+L n+ k v +k+++++i n++p+i lcl|FitnessBrowser__Pedo557:CA265_RS15395 136 KPLHDKYKIKRVVVSTYQSVTGTGVKAVEQLMNERKGVD------------GPKAYPYEIDLNVLPHI 191 *********************************998763............3589************* PP TIGR01296 205 dklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeap 272 d ++e+Gytkee+k++ et+ki+ ++ +kv+at+vr+Pv+ ghsesv+iefe+++++ ev+ +L+++p lcl|FitnessBrowser__Pedo557:CA265_RS15395 192 DVFMENGYTKEEMKMVKETNKIMSDDSIKVTATTVRIPVMGGHSESVNIEFENDFDLAEVRSILEKSP 259 ******************************************************************** PP TIGR01296 273 gvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 g++v+dd + +yp+P +a +kdevfvgrir+D s k+l+l++vaDnlrkGaa+navqiae li+ lcl|FitnessBrowser__Pedo557:CA265_RS15395 260 GIIVVDDVANLKYPMPKDAHEKDEVFVGRIRRDESAPKALNLWIVADNLRKGAATNAVQIAEYLIQ 325 ***************************************************************987 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 3.47 // [ok]
This GapMind analysis is from Apr 09 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