Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate Echvi_2395 Echvi_2395 dihydrodipicolinate reductase
Query= reanno::Cola:Echvi_2395 (240 letters) >FitnessBrowser__Cola:Echvi_2395 Length = 240 Score = 483 bits (1242), Expect = e-141 Identities = 240/240 (100%), Positives = 240/240 (100%) Query: 1 MNILILGYGKMGKIISQIAEERGHTIAAKIDESNIHELDKLDTTKVDAAIEFSQPDAAVQ 60 MNILILGYGKMGKIISQIAEERGHTIAAKIDESNIHELDKLDTTKVDAAIEFSQPDAAVQ Sbjct: 1 MNILILGYGKMGKIISQIAEERGHTIAAKIDESNIHELDKLDTTKVDAAIEFSQPDAAVQ 60 Query: 61 NLSWAIKHNIPVVCGTTGWLDKKPEIERLTLSNGGAFFYASNYSIGVNILFKVNSFLAKI 120 NLSWAIKHNIPVVCGTTGWLDKKPEIERLTLSNGGAFFYASNYSIGVNILFKVNSFLAKI Sbjct: 61 NLSWAIKHNIPVVCGTTGWLDKKPEIERLTLSNGGAFFYASNYSIGVNILFKVNSFLAKI 120 Query: 121 MNEQPAYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDRVKRWDLDKDVNGNEHSLPIT 180 MNEQPAYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDRVKRWDLDKDVNGNEHSLPIT Sbjct: 121 MNEQPAYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDRVKRWDLDKDVNGNEHSLPIT 180 Query: 181 AKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKKGVLSMDDYLTF 240 AKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKKGVLSMDDYLTF Sbjct: 181 AKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKKGVLSMDDYLTF 240 Lambda K H 0.317 0.134 0.390 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: 370 Number of extensions: 11 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: 240 Length of database: 240 Length adjustment: 23 Effective length of query: 217 Effective length of database: 217 Effective search space: 47089 Effective search space used: 47089 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 Echvi_2395 Echvi_2395 (dihydrodipicolinate reductase)
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.19223.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-43 133.5 0.2 1.2e-42 132.3 0.2 1.6 1 lcl|FitnessBrowser__Cola:Echvi_2395 Echvi_2395 dihydrodipicolinate r Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2395 Echvi_2395 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 132.3 0.2 1.2e-42 1.2e-42 61 268 .. 34 237 .. 1 239 [. 0.86 Alignments for each domain: == domain 1 score: 132.3 bits; conditional E-value: 1.2e-42 TIGR00036 61 dleavkvlaekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiG 134 +++ ++l +k+d i+f++p+a+++n+ a+++++ +V GTTG ++ + e++ l+ +g a +a+N++iG lcl|FitnessBrowser__Cola:Echvi_2395 34 NIHELDKLDTTKVDAAIEFSQPDAAVQNLSWAIKHNIPVVCGTTGWLDK-KPEIERLTLSNGGAFFYASNYSIG 106 33444467799**********************************9875.689********************* PP TIGR00036 135 vnlllkllekaakvled...vDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkke 205 vn+l+k+ +ak++++ + + + E+HH +KkDaPSGTA+ lae i + ++ +k+ + + ++G+ + lcl|FitnessBrowser__Cola:Echvi_2395 107 VNILFKVNSFLAKIMNEqpaYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDR-VKRW--DLDKDVNGNE--H 175 ***************98443589999**********************999995.3333..3334456655..7 PP TIGR00036 206 eiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledv 268 + i+a R g h v++ s+ + +ei+H+a+sR+ fa G+v++++w++dk+ +v ++d lcl|FitnessBrowser__Cola:Echvi_2395 176 SLPITAKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKK-GVLSMDDY 237 8899***********************************************986.56677776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (240 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: 00:00:00.02 # Mc/sec: 2.97 // [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