Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_007154190.1 MDG893_RS12695 1-phosphofructokinase
Query= reanno::pseudo5_N2C3_1:AO356_07330 (313 letters) >NCBI__GCF_000170835.1:WP_007154190.1 Length = 330 Score = 256 bits (655), Expect = 4e-73 Identities = 146/291 (50%), Positives = 180/291 (61%) Query: 1 MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60 MA++LT+TLNPALDL E + G VNRS + AAGKG+N+ +VL LGHT+TVSG Sbjct: 1 MARVLTITLNPALDLNAETDSMRLGNVNRSRSTRLEAAGKGINLGRVLTRLGHTVTVSGL 60 Query: 61 LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120 LG+ NA F+ LF+ D F+R+PG+ R N+K+AE GR+TDLNGPG V A A L Sbjct: 61 LGDINAAPFDRLFSSDILADHFVRIPGQNRINVKIAESGGRVTDLNGPGFDVPADALDRL 120 Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180 ARL + D V +AGSLP G P+ L L+ + + V LDTSG L L A P Sbjct: 121 KARLGDLKSRFDAVAIAGSLPGGFPPEALAELVTLAREADIPVWLDTSGAGLTAGLKALP 180 Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240 IKPN EELA+ G + S A A+A + L A GI +VVIS G GV W S A Sbjct: 181 DGIKPNMEELAEWAGHPLESLDAIAEAGRSLQATGIANVVISMGEKGVLWLSPKGNWQAL 240 Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFG 291 PP V+ STV AGD+LLAGM+HGLL PEQ L TATA++A V IG G Sbjct: 241 PPPVTATSTVCAGDTLLAGMIHGLLEHHHPEQVLSTATALSAECVRHIGVG 291 Lambda K H 0.317 0.132 0.373 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: 300 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: 313 Length of database: 330 Length adjustment: 28 Effective length of query: 285 Effective length of database: 302 Effective search space: 86070 Effective search space used: 86070 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_007154190.1 MDG893_RS12695 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))
# 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.carbon/TIGR03828.hmm # target sequence database: /tmp/gapView.3428827.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03828 [M=305] Accession: TIGR03828 Description: pfkB: 1-phosphofructokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-95 303.7 0.0 7.2e-95 303.5 0.0 1.0 1 NCBI__GCF_000170835.1:WP_007154190.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000170835.1:WP_007154190.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 303.5 0.0 7.2e-95 7.2e-95 1 304 [. 4 307 .. 4 308 .. 0.98 Alignments for each domain: == domain 1 score: 303.5 bits; conditional E-value: 7.2e-95 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 +lT+TlNpa+D+ e+++++lg+vnr +s+rl+a+GKGin rvL++lg++v+++g+lG +++++++l++++ NCBI__GCF_000170835.1:WP_007154190.1 4 VLTITLNPALDLNAETDSMRLGNVNRSRSTRLEAAGKGINLGRVLTRLGHTVTVSGLLGDINAAPFDRLFSSD 76 79*********************************************************************** PP TIGR03828 74 giktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedly 146 ++++fv+++g+ Rinvki+es g++t+ln+pG+ + +++l++l+++l + ++ d + +aGSlP g p++++ NCBI__GCF_000170835.1:WP_007154190.1 77 ILADHFVRIPGQNRINVKIAESGGRVTDLNGPGFDVPADALDRLKARLGDLKSRFDAVAIAGSLPGGFPPEAL 149 *************************************************99999******************* PP TIGR03828 147 aelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlis 219 ael+ l+re++++v lDtsg+ L+++lka p+ iKPN eEl+e++g+ l++ +++ ea+r l++ g++nv+is NCBI__GCF_000170835.1:WP_007154190.1 150 AELVTLAREADIPVWLDTSGAGLTAGLKALPDGIKPNMEELAEWAGHPLESLDAIAEAGRSLQATGIANVVIS 222 ************************************************************************* PP TIGR03828 220 lGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdl 292 +G++G+l+++++g ++a +p +++ stv+AGD+++Ag++++l +++++e++l++a+A++a+ + + g++ p NCBI__GCF_000170835.1:WP_007154190.1 223 MGEKGVLWLSPKGNWQALPPPVTATSTVCAGDTLLAGMIHGLLEHHHPEQVLSTATALSAECVRHIGVGDPMA 295 *******************************************************************888888 PP TIGR03828 293 edieelleevki 304 +d +l +++++ NCBI__GCF_000170835.1:WP_007154190.1 296 DDFIQLIQQTRV 307 888888888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (330 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.28 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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