Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate 352847 BT3320 dihydrodipicolinate reductase (NCBI ptt file)
Query= reanno::Pedo557:CA265_RS15670 (244 letters) >FitnessBrowser__Btheta:352847 Length = 254 Score = 230 bits (586), Expect = 2e-65 Identities = 120/252 (47%), Positives = 161/252 (63%), Gaps = 12/252 (4%) Query: 1 MKLALLGYGKMGQIIEKFAVERGHEIVLKITIDNQEDLTRQNLKSADVAIDFSTPDSVLK 60 MK+AL+GYGKMG+ +EK A+ RGHEIV I +DNQED + KSADVAI+F+ P Sbjct: 1 MKIALIGYGKMGKELEKAALSRGHEIVCIIDVDNQEDFESEAFKSADVAIEFTNPMVAYS 60 Query: 61 NIDACFDANVPIVVGTTGWYGKL-QEVKDDCNNSNNTLLYGSNFSIGVNLFFKLNQTLAK 119 N F A V +V G+TGW + +E+K C TL + SNFS+GV +F +N+ LAK Sbjct: 61 NYMKAFKAGVKLVSGSTGWMAEHGEEIKKLCTEGGKTLFWSSNFSLGVAIFSSVNKYLAK 120 Query: 120 LMNNYPAYEVQVEEIHHTQKLDAPSGTAITLAEGIVDNLDRKQEWL--------NEVVGT 171 +MN +P Y+V + E HH KLDAPSGTAITLAEGI++N+DRK +W+ V GT Sbjct: 121 IMNQFPGYDVTMSETHHIHKLDAPSGTAITLAEGILENMDRKDKWVKGTLLAPDGTVSGT 180 Query: 172 DVELFPKAEQLLIESHRIENIPGTHTVIYSSEVDEIEIKHTAHNRAGFALGAVVAAEWLK 231 D + + I+S R + G HT+ Y SEVD I I H A NR GF LGA++AAE+ Sbjct: 181 DA---CASNEFPIDSIREGEVFGIHTIRYESEVDSISITHDAKNRGGFVLGAILAAEYTA 237 Query: 232 DKKGFFSITDIF 243 +G+ ++D+F Sbjct: 238 QHEGYLGMSDLF 249 Lambda K H 0.317 0.135 0.389 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: 204 Number of extensions: 12 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: 244 Length of database: 254 Length adjustment: 24 Effective length of query: 220 Effective length of database: 230 Effective search space: 50600 Effective search space used: 50600 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: 41 (21.6 bits) S2: 46 (22.3 bits)
Align candidate 352847 BT3320 (dihydrodipicolinate reductase (NCBI ptt file))
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
# 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/TIGR00036.hmm # target sequence database: /tmp/gapView.31589.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00036 [M=270] Accession: TIGR00036 Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-45 142.2 0.3 5.3e-44 136.7 0.3 2.0 1 lcl|FitnessBrowser__Btheta:352847 BT3320 dihydrodipicolinate reduc Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:352847 BT3320 dihydrodipicolinate reductase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 136.7 0.3 5.3e-44 5.3e-44 59 268 .. 35 248 .. 1 250 [. 0.84 Alignments for each domain: == domain 1 score: 136.7 bits; conditional E-value: 5.3e-44 TIGR00036 59 eddleavkvlaekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiG 134 ++d e a k+adv i+ft p +++n a ++gv+lV+G TG e+ +e+k+l + g +l ++Nf++G lcl|FitnessBrowser__Btheta:352847 35 QEDFE---SEAFKSADVAIEFTNPMVAYSNYMKAFKAGVKLVSGSTGWMAEHGEEIKKLCTEGGKTLFWSSNFSLG 107 33333...3367899************************************************************* PP TIGR00036 135 vnlllkllekaakvledv...DiEiiElHHrhKkDaPSGTAlklaeiiakarg.kd..lkeaaveeregltGerk. 203 v ++ + +++ak+++++ D+ + E+HH hK DaPSGTA+ lae i ++ + kd +k ++ +++G lcl|FitnessBrowser__Btheta:352847 108 VAIFSSVNKYLAKIMNQFpgyDVTMSETHHIHKLDAPSGTAITLAEGILENMDrKDkwVKGTLLAPDGTVSGTDAc 183 *************99985555***************************9998833311345556666677776651 PP TIGR00036 204 .keeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledv 268 ++e i ++R g+v g ht+ + s+ + + itH+a++R f+ G+++a+++ ++ e + +++d+ lcl|FitnessBrowser__Btheta:352847 184 aSNEFPIDSIREGEVFGIHTIRYESEVDSISITHDAKNRGGFVLGAILAAEYTAQHE-GYLGMSDL 248 155556*********************************************988765.56677666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (254 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 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 2.64 // [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