Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate AZOBR_RS30840 AZOBR_RS30840 hypothetical protein
Query= reanno::psRCH2:GFF3290 (312 letters) >FitnessBrowser__azobra:AZOBR_RS30840 Length = 323 Score = 209 bits (531), Expect = 9e-59 Identities = 128/313 (40%), Positives = 175/313 (55%), Gaps = 6/313 (1%) Query: 4 VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLG-----HQLTVT 58 V+TVTLN A+D T+ +P G VNR+ + A GKG+NVA LA +T T Sbjct: 11 VVTVTLNAAIDQTLDVPGFAAGAVNRAVAETRTAGGKGINVAAFLAGASLAGGATPVTAT 70 Query: 59 GFLGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGR-VTDINGPGLAVSEAQR 117 GFLGE N F+ LF RG D +R+AG +R N+KL + +G VTDIN PGL V Sbjct: 71 GFLGEENTAVFDALFRRRGIRDRCLRLAGRSRVNIKLVDREGHSVTDINLPGLHVPAESW 130 Query: 118 AELLARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLA 177 LL + L + V++GS+P G+ + +++ +L G V +D SG LR +A Sbjct: 131 RGLLTVVDDLAVTNRTFVLSGSVPAGVPDTAYTEMVTALHRRGAFVVVDASGPPLRHAVA 190 Query: 178 TRPWLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAAL 237 RP ++KPN ELAE G L + + A+ L E GI VVVS GA+G + G AL Sbjct: 191 ARPDMVKPNAAELAELLGRPLKDRAEVVRAARELSESGIALVVVSLGAEGAVFVEGGRAL 250 Query: 238 HASPPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQ 297 A PP V V STVGAGD+++AG++ LEG E TA AA + ++G + + Sbjct: 251 LAMPPPVEVASTVGAGDAMVAGVVAARLEGMGLEDCARRGTAFAAGTLSRLGPELPPPER 310 Query: 298 LAELQAAVRLQPL 310 LAEL AVR++ L Sbjct: 311 LAELMRAVRVEEL 323 Lambda K H 0.316 0.132 0.371 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: 251 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: 312 Length of database: 323 Length adjustment: 27 Effective length of query: 285 Effective length of database: 296 Effective search space: 84360 Effective search space used: 84360 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: 48 (23.1 bits)
Align candidate AZOBR_RS30840 AZOBR_RS30840 (hypothetical protein)
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.23423.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-96 308.9 0.2 1.9e-96 308.7 0.2 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS30840 AZOBR_RS30840 hypothetical prote Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS30840 AZOBR_RS30840 hypothetical protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.7 0.2 1.9e-96 1.9e-96 1 305 [] 11 321 .. 11 321 .. 0.97 Alignments for each domain: == domain 1 score: 308.7 bits; conditional E-value: 1.9e-96 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklg.....vevvalgflGgftge 64 ++TvTlN+aiD+t+++ ++ +g+vnr+ +e agGKGinVa +L+ + ++v+a+gflG+++ + lcl|FitnessBrowser__azobra:AZOBR_RS30840 11 VVTVTLNAAIDQTLDVPGFAAGAVNRAVAETRTAGGKGINVAAFLAGASlaggaTPVTATGFLGEENTA 79 79******************************************9977522222689************ PP TIGR03828 65 eiealleeegiktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlv 132 ++al++++gi +++++++g +R+n+k++++ + +t++n pG ++ +e + ll+ +++ + +++++v lcl|FitnessBrowser__azobra:AZOBR_RS30840 80 VFDALFRRRGIRDRCLRLAGRSRVNIKLVDReGHSVTDINLPGLHVPAESWRGLLTVVDDLAVTNRTFV 148 *******************************9999********************************** PP TIGR03828 133 laGSlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeev 201 l+GS+P+gvp+++y e++ +l+++ga v++D+sg++L+++++a+p+++KPN++El+ellgr lk+ +ev lcl|FitnessBrowser__azobra:AZOBR_RS30840 149 LSGSVPAGVPDTAYTEMVTALHRRGAFVVVDASGPPLRHAVAARPDMVKPNAAELAELLGRPLKDRAEV 217 ********************************************************************* PP TIGR03828 202 ieaarkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleea 270 ++aar+l e+g++ v++slGa+Ga++v+ +al a +p +ev+stvGAGD+mvAg+++a +g+ le++ lcl|FitnessBrowser__azobra:AZOBR_RS30840 218 VRAARELSESGIALVVVSLGAEGAVFVEGGRALLAMPPPVEVASTVGAGDAMVAGVVAARLEGMGLEDC 286 ********************************************************************* PP TIGR03828 271 lrlavAvgaaaassegtelpdledieelleevkie 305 r ++A++a + s+ g elp +e+++el + v++e lcl|FitnessBrowser__azobra:AZOBR_RS30840 287 ARRGTAFAAGTLSRLGPELPPPERLAELMRAVRVE 321 ********************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (323 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.79 // [ok]
This GapMind analysis is from Sep 17 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