Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_012383424.1 BIND_RS02095 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_000019845.1:WP_012383424.1 Length = 431 Score = 337 bits (864), Expect = 4e-97 Identities = 181/406 (44%), Positives = 253/406 (62%), Gaps = 1/406 (0%) Query: 16 EAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLS 75 +A+ ++ +L + S + KN AL A+ L + + +L AN +DL + Q AF+DRL+ Sbjct: 25 QARASAHALSLASTEAKNLALRVAAEQLRKRTQDLLLANARDLEGAKAQDANAAFLDRLT 84 Query: 76 LSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTV 135 L +RI A+GL ++A L DP G+ L+ + NGL +E+V PLGVIG+IYE+RP VT Sbjct: 85 LDDKRIEAIARGLDEIAALPDPVGRMLARYERPNGLVIERVATPLGVIGIIYESRPAVTA 144 Query: 136 DATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQL 195 DA L LK+GNA +L+GGS + S I + + L +P+ +V + + DRAA ++ Sbjct: 145 DAGALCLKAGNAAILRGGSESFFSATIIHACLTEGLRAAGLPEAAVSLVPTRDRAAVGEM 204 Query: 196 FT-MKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAK 254 + +DV++PRGG L+ V A VPV G HI++ + AD+EKA I+ NAK Sbjct: 205 LKGLDGTIDVIVPRGGKSLVARVQAEARVPVFAHLEGVNHIFVHRAADLEKAAIIIRNAK 264 Query: 255 TDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGEDDWK 314 RP VC AAE L+V + +A H L L + GD TI P A E DW+ Sbjct: 265 LRRPGVCGAAEILLVDEACMATHLAPLTRMLLDAGCAIRGDAATQTIDPRVTAAMESDWR 324 Query: 315 NEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNAST 374 EY IAV+ +D L AIAHIET+G+ H++ I+TE+QEAAD+FLA VD+A + HNAST Sbjct: 325 TEYSDAIIAVRVIDGLNKAIAHIETHGSHHTDCIITEDQEAADRFLAEVDSAIVMHNAST 384 Query: 375 RFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 +F DGG GFGAEIGI+T +LHARGP+GL LT+ K+ + G GQIR Sbjct: 385 QFADGGEFGFGAEIGIATGRLHARGPVGLEQLTSFKYRVHGNGQIR 430 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: 470 Number of extensions: 20 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: 431 Length adjustment: 32 Effective length of query: 388 Effective length of database: 399 Effective search space: 154812 Effective search space used: 154812 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_012383424.1 BIND_RS02095 (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.2041456.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-132 427.7 0.4 2.4e-132 427.4 0.4 1.0 1 NCBI__GCF_000019845.1:WP_012383424.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019845.1:WP_012383424.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.4 0.4 2.4e-132 2.4e-132 1 398 [] 26 420 .. 26 420 .. 0.98 Alignments for each domain: == domain 1 score: 427.4 bits; conditional E-value: 2.4e-132 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 a+ +a l st+ kn al + a++L+++++ +l ana+d++ ak++ a+ldrL+L++++++ ia ++ NCBI__GCF_000019845.1:WP_012383424.1 26 ARASAHALSLASTEAKNLALRVAAEQLRKRTQDLLLANARDLEGAKAQDANAAFLDRLTLDDKRIEAIARGLD 98 78889999***************************************************************** PP TIGR00407 74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146 +++ L+dPvG+++ e+ +GL++erv +PlGv+g+iye+rP v++d+ +Lclk+Gna+iL+Gg+e+ +s + NCBI__GCF_000019845.1:WP_012383424.1 99 EIAALPDPVGRMLARYERPNGLVIERVATPLGVIGIIYESRPAVTADAGALCLKAGNAAILRGGSESFFSATI 171 ************************************************************************* PP TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellk.ldeyvdlliPrGgnelvklikeestiPvlehadGvCh 218 + + + + l+ +glp av l+ + dr+ v e+lk ld +d+++PrGg++lv ++ e+++Pv+ h +Gv h NCBI__GCF_000019845.1:WP_012383424.1 172 IHACLTEGLRAAGLPEAAVSLVPTRDRAAVGEMLKgLDGTIDVIVPRGGKSLVARVQAEARVPVFAHLEGVNH 244 **********************************769************************************ PP TIGR00407 219 iyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlklleleka 291 i++ + adl+ka +i +ak +rP +C a e LLv++a + +l L++ l ++g +r+da+++ + + NCBI__GCF_000019845.1:WP_012383424.1 245 IFVHRAADLEKAAIIIRNAKLRRPGVCGAAEILLVDEACMATHLAPLTRMLLDAGCAIRGDAATQTIDPRV-- 315 ****************************************************************9998876.. PP TIGR00407 292 teaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrf 364 +++++ d+++e+++ +++v++++ l++ai+hi+++g++h+d+i+ted+++a++f+ evdsa v +nast+f NCBI__GCF_000019845.1:WP_012383424.1 316 --TAAMESDWRTEYSDAIIAVRVIDGLNKAIAHIETHGSHHTDCIITEDQEAADRFLAEVDSAIVMHNASTQF 386 ..345678***************************************************************** PP TIGR00407 365 adGfrfGfGaevgistqklharGPvGLeaLvsyk 398 adG++fGfGae+gi+t +lharGPvGLe L+s+k NCBI__GCF_000019845.1:WP_012383424.1 387 ADGGEFGFGAEIGIATGRLHARGPVGLEQLTSFK 420 ********************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (431 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 16.59 // [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