Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_013259204.1 DEBA_RS12005 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_000143965.1:WP_013259204.1 Length = 418 Score = 370 bits (950), Expect = e-107 Identities = 194/405 (47%), Positives = 262/405 (64%) Query: 16 EAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLS 75 +A++A++ + + KN AL +A ++E++ A+ A N D+ GRE G + A +DRL+ Sbjct: 13 QARQAARRVAVAPSDRKNAALLLLAKLIEQNKAALQAENAIDVAAGREAGLSAAMIDRLT 72 Query: 76 LSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTV 135 LS I AQGLR+VA L DP G+ + W NGLQV + +PLGVIG IYE+RPNVTV Sbjct: 73 LSDGVIAGMAQGLREVAALPDPVGEMTAMWRRPNGLQVGRQRIPLGVIGFIYESRPNVTV 132 Query: 136 DATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQL 195 DA L LKSGNA+VLKGG A+ SN A+ +I +AL ++++P +VQ I +TDRAAT L Sbjct: 133 DAAALCLKSGNAVVLKGGKEALRSNLALGRLIAQALEQSQLPAHAVQVIDTTDRAATLAL 192 Query: 196 FTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAKT 255 E +DV+IPRGG LI+ V + +PVL+ G CH+++D+ AD+ AI I VN+K Sbjct: 193 LKQDELIDVIIPRGGESLIRFVAAESRIPVLKHYKGVCHVFVDRGADIAMAIDICVNSKC 252 Query: 256 DRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGEDDWKN 315 RP VCNA ET++VH D AL + + G L I P A PA +DDW Sbjct: 253 HRPGVCNAMETMLVHADIAESFLPRCAEALILRGVELRGCPRTLAIAPQAKPANDDDWPA 312 Query: 316 EYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNASTR 375 E+L +AV+ VD L +A+ HI YG++H+EAIVT + A +F+ VD++ + NASTR Sbjct: 313 EFLDLILAVRVVDSLEEAMDHIARYGSQHTEAIVTRDYARARRFIDGVDSSLVLVNASTR 372 Query: 376 FTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 F DGG LG GAEIGI+T KLHA GPMGL LTT KF+ G GQ+R Sbjct: 373 FNDGGQLGLGAEIGINTSKLHAFGPMGLTELTTTKFVALGNGQVR 417 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: 427 Number of extensions: 17 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: 420 Length of database: 418 Length adjustment: 32 Effective length of query: 388 Effective length of database: 386 Effective search space: 149768 Effective search space used: 149768 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: 50 (23.9 bits)
Align candidate WP_013259204.1 DEBA_RS12005 (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.6852.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-148 478.6 0.1 7.8e-148 478.5 0.1 1.0 1 lcl|NCBI__GCF_000143965.1:WP_013259204.1 DEBA_RS12005 glutamate-5-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_013259204.1 DEBA_RS12005 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.5 0.1 7.8e-148 7.8e-148 1 398 [] 14 407 .. 14 407 .. 0.99 Alignments for each domain: == domain 1 score: 478.5 bits; conditional E-value: 7.8e-148 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a++aa ++a ++ kn al ++a+ ++++ ++ a+na+d+aa++e Gl+ a++drL+L+++ + ++a lcl|NCBI__GCF_000143965.1:WP_013259204.1 14 ARQAARRVAVAPSDRKNAALLLLAKLIEQNKAALQAENAIDVAAGREAGLSAAMIDRLTLSDGVIAGMA 82 89******************************************************************* PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 +++++v+ L+dPvG+++ ++ +GL++ r r+PlGv+g iye+rP+v+vd+a+Lclk+Gnav+LkGgk lcl|NCBI__GCF_000143965.1:WP_013259204.1 83 QGLREVAALPDPVGEMTAMWRRPNGLQVGRQRIPLGVIGFIYESRPNVTVDAAALCLKSGNAVVLKGGK 151 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 ea rsn al ++i +aleq+ lp++avq+i+++dr+ llk+de +d++iPrGg++l++ + es+i lcl|NCBI__GCF_000143965.1:WP_013259204.1 152 EALRSNLALGRLIAQALEQSQLPAHAVQVIDTTDRAATLALLKQDELIDVIIPRGGESLIRFVAAESRI 220 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pvl+h +GvCh+++d+ ad+a+a+ + v++k +rP +Cna+et+Lv+ +iae+fl++ +++l gvel lcl|NCBI__GCF_000143965.1:WP_013259204.1 221 PVLKHYKGVCHVFVDRGADIAMAIDICVNSKCHRPGVCNAMETMLVHADIAESFLPRCAEALILRGVEL 289 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+ +l++ +++k + ++d+ efl+l+L+v++v++leea++hi +yg++h++ai+t+d + a+ lcl|NCBI__GCF_000143965.1:WP_013259204.1 290 RGCPRTLAIAPQAKP----ANDDDWPAEFLDLILAVRVVDSLEEAMDHIARYGSQHTEAIVTRDYARAR 354 *****9999998843....34689********************************************* PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f++ vds+ v vnastrf dG++ G+Gae+gi t+klha GP+GL L+++k lcl|NCBI__GCF_000143965.1:WP_013259204.1 355 RFIDGVDSSLVLVNASTRFNDGGQLGLGAEIGINTSKLHAFGPMGLTELTTTK 407 **************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (418 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: 7.28 // [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