Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_028951072.1 Q385_RS0107505 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_000619805.1:WP_028951072.1 Length = 446 Score = 379 bits (973), Expect = e-109 Identities = 198/418 (47%), Positives = 282/418 (67%), Gaps = 8/418 (1%) Query: 11 EAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAF 70 E+ A +AKK ++ L L+ KN AL A++L+++ + IL N+KDL N ++G+T+A Sbjct: 8 ESIAKKAKKTTRQLSSLTTDIKNKALLKTAELLDKNRQLILQENQKDLENAEKKGYTKAL 67 Query: 71 MDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEAR 130 +DRL+L+ +RI Q L+DVA L DP G+ ++ WT NGL+V ++ VPLGVI +IYEAR Sbjct: 68 LDRLALNDKRIDQMIQVLKDVAALPDPVGEIINMWTRPNGLKVGQMRVPLGVILIIYEAR 127 Query: 131 PNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRA 190 PNVT++A L +KS NA++LKGGS INSN+ +VE+I +A ET P+++V F+ +TDR Sbjct: 128 PNVTIEAASLCMKSSNAVILKGGSETINSNRVLVEIIKQACRETCFPEDAVMFVDTTDRN 187 Query: 191 ATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISIL 250 N+L ++ +DV IPRGG LI+AV EN+ +PV++ G C++YID +AD+EKA++I Sbjct: 188 IVNELLKLEGLIDVAIPRGGESLIRAVAENSRIPVIKHYKGVCNLYIDDEADMEKALNIA 247 Query: 251 VNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTII-------- 302 NAK RP+VCNA E L+V+K + E+ K + + DE+ ++ Sbjct: 248 YNAKVQRPSVCNAIENLVVNKKIADKFLPEIAYYYGKAGVEMRCDEYSYNLLINHPKAKD 307 Query: 303 PDAVPAGEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAI 362 + +PA E+D+ E+L IAVK V+DL +AI IE YG+ HS+AIVTEN KF+ Sbjct: 308 TEILPAKEEDYYEEFLDLIIAVKVVEDLDEAIDFIEKYGSHHSDAIVTENYTKGMKFIQQ 367 Query: 363 VDAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 VD+AA+Y NASTRFTDG G GAE+GIST K+HARGPM L LT KF++ G GQ+R Sbjct: 368 VDSAAVYINASTRFTDGNEFGLGAEMGISTDKIHARGPMALKELTIPKFIIFGDGQLR 425 Lambda K H 0.315 0.131 0.365 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: 464 Number of extensions: 23 Number of successful extensions: 2 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: 420 Length of database: 446 Length adjustment: 32 Effective length of query: 388 Effective length of database: 414 Effective search space: 160632 Effective search space used: 160632 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: 51 (24.3 bits)
Align candidate WP_028951072.1 Q385_RS0107505 (glutamate-5-semialdehyde dehydrogenase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))
# 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/TIGR00407.hmm # target sequence database: /tmp/gapView.2336.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00407 [M=398] Accession: TIGR00407 Description: proA: glutamate-5-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-154 501.0 2.4 1.3e-154 500.7 2.4 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028951072.1 Q385_RS0107505 glutamate-5-semia Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028951072.1 Q385_RS0107505 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 500.7 2.4 1.3e-154 1.3e-154 1 395 [. 14 412 .. 14 415 .. 0.97 Alignments for each domain: == domain 1 score: 500.7 bits; conditional E-value: 1.3e-154 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 ak+ + +l +l+t+ kn+al k a+ L ++ +lil++n+kd+++a+++G ++alldrL+L+++++ +++ lcl|NCBI__GCF_000619805.1:WP_028951072.1 14 AKKTTRQLSSLTTDIKNKALLKTAELLDKNRQLILQENQKDLENAEKKGYTKALLDRLALNDKRIDQMI 82 89999**************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 + +kdv+ L+dPvG++i+ ++ +GLk+ ++rvPlGv+++iyearP+v++++asLc+k+ naviLkGg+ lcl|NCBI__GCF_000619805.1:WP_028951072.1 83 QVLKDVAALPDPVGEIINMWTRPNGLKVGQMRVPLGVILIIYEARPNVTIEAASLCMKSSNAVILKGGS 151 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 e+++sn++lve+i++a ++t p av ++++dr+ v+ellkl+ +d+ iPrGg++l++ + e+s+i lcl|NCBI__GCF_000619805.1:WP_028951072.1 152 ETINSNRVLVEIIKQACRETCFPEDAVMFVDTTDRNIVNELLKLEGLIDVAIPRGGESLIRAVAENSRI 220 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pv++h +GvC++y+d++ad++ka ++ +ak qrPs+Cnaie L+vnk+ia++fl+e++ ++gve+ lcl|NCBI__GCF_000619805.1:WP_028951072.1 221 PVIKHYKGVCNLYIDDEADMEKALNIAYNAKVQRPSVCNAIENLVVNKKIADKFLPEIAYYYGKAGVEM 289 ********************************************************************* PP TIGR00407 277 radalvlkll.elekateae...vskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedk 341 r d++ +ll + ka+++e +++ed+ +efl+l+++vk+vedl+eai+ i++yg++hsdai+te+ lcl|NCBI__GCF_000619805.1:WP_028951072.1 290 RCDEYSYNLLiNHPKAKDTEilpAKEEDYYEEFLDLIIAVKVVEDLDEAIDFIEKYGSHHSDAIVTENY 358 ****99987524444444432226788****************************************** PP TIGR00407 342 knaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLv 395 ++ kf+++vdsaavy nastrf+dG +fG+Gae+gist+k+harGP+ L+ L+ lcl|NCBI__GCF_000619805.1:WP_028951072.1 359 TKGMKFIQQVDSAAVYINASTRFTDGNEFGLGAEMGISTDKIHARGPMALKELT 412 ***************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (446 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.99 // [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