Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 8501129 DvMF_1865 acetate kinase (RefSeq)
Query= BRENDA::Q9WYB1 (403 letters) >FitnessBrowser__Miya:8501129 Length = 404 Score = 422 bits (1085), Expect = e-123 Identities = 216/403 (53%), Positives = 283/403 (70%), Gaps = 8/403 (1%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-----GDEKHVIERE 55 M VLVINSGSSSIKYQLI+M EK LC G+ ERIG +L H++ +EK V+E+ Sbjct: 1 MNVLVINSGSSSIKYQLIDMTTEKALCSGLVERIGEGMGKLTHKIKPDTDAEEKIVLEQA 60 Query: 56 LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115 +H E +K +++ + D GVI D EI AVGHRV+ GGE K+SV +DE I + Sbjct: 61 FANHVEGMKKVVDLITDADKGVIADKGEIYAVGHRVLLGGEEIKQSVKIDEWAKGIIRDY 120 Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175 PL PLHNPANL GI+ A +L P P+V VFDT FHQT+P+KAYLY +PY+ Y+ +IRR Sbjct: 121 IPLGPLHNPANLAGIEVAEELFPHAPSVGVFDTEFHQTMPKKAYLYPLPYDLYKTLRIRR 180 Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235 YGFHGTSHRY++K+ AE LGK L+EL IITCH+GNG S+AAVK G+CVDT+MG TPLEGL Sbjct: 181 YGFHGTSHRYITKKTAEFLGKPLDELNIITCHLGNGCSMAAVKNGRCVDTTMGITPLEGL 240 Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295 +MGTR GD+DPA+ F+MEK+G S E+ ++NK+SG+ G+ +DMRDI A KGD Sbjct: 241 MMGTRCGDIDPALVPFLMEKKGWSGAEIDTVMNKQSGLKGICG--MNDMRDIHAAREKGD 298 Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355 E +L +++ YRI KYIG++A + +DAIVFTAG+GEN + R VC ++ LG+ +D Sbjct: 299 EMAELAFQMFVYRIRKYIGSFAVVVGKLDAIVFTAGIGENDDLVRAAVCKDMDILGIDID 358 Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398 + N + G+ I P RV VLVVPTNEEL IA+ T ++ Sbjct: 359 EAVNAKR-SGQARHIGKPGQRVPVLVVPTNEELEIAQTTVAVL 400 Lambda K H 0.318 0.138 0.391 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: 498 Number of extensions: 16 Number of successful extensions: 4 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: 403 Length of database: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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: 50 (23.9 bits)
Align candidate 8501129 DvMF_1865 (acetate kinase (RefSeq))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))
# 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/TIGR00016.hmm # target sequence database: /tmp/gapView.26101.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00016 [M=405] Accession: TIGR00016 Description: ackA: acetate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-148 480.9 0.0 1.6e-148 480.7 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501129 DvMF_1865 acetate kinase (RefSeq Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501129 DvMF_1865 acetate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 480.7 0.0 1.6e-148 1.6e-148 5 402 .. 2 398 .. 1 401 [. 0.95 Alignments for each domain: == domain 1 score: 480.7 bits; conditional E-value: 1.6e-148 TIGR00016 5 kilvlnaGssslkfalldaensekvllsglverikle..eariktv..edgekkeeeklaiedheeavkkllntlkk 77 +lv+n+Gsss+k++l+d++ +ek l+sglveri + + k++ +d+e+k ++a+++h e++kk+++ +++ lcl|FitnessBrowser__Miya:8501129 2 NVLVINSGSSSIKYQLIDMT-TEKALCSGLVERIGEGmgKLTHKIKpdTDAEEKIVLEQAFANHVEGMKKVVDLITD 77 79******************.69999*******97541133223333388899999999*****************9 PP TIGR00016 78 .dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFD 153 dk ++ ++ ei ++GHRv Gge+ ++sv +++ + i+d ++l PlHnpa+l gie + + ++a+ v vFD lcl|FitnessBrowser__Miya:8501129 78 aDKGVIADKGEIYAVGHRVLLGGEEIKQSVKIDEWAKGIIRDYIPLGPLHNPANLAGIEVAE--ELFPHAPSVGVFD 152 999***********************************************************..7778899****** PP TIGR00016 154 tafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksid 230 t fHqt+p++aylY+lPy+lyk l +RrYGfHGtsh+y+t+++a+ l+kpld+ln+i+cHlGnG s++avknG+++d lcl|FitnessBrowser__Miya:8501129 153 TEFHQTMPKKAYLYPLPYDLYKTLRIRRYGFHGTSHRYITKKTAEFLGKPLDELNIITCHLGNGCSMAAVKNGRCVD 229 ***************************************************************************** PP TIGR00016 231 tsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAl 307 t+mG+tPLeGl+mGtR+GdiDpa++ +l+e++g s +ei +++nk+sGl gi g +D+Rdi ++ e+g+e a+lA+ lcl|FitnessBrowser__Miya:8501129 230 TTMGITPLEGLMMGTRCGDIDPALVPFLMEKKGWSGAEIDTVMNKQSGLKGICG-MNDMRDIHAAREKGDEMAELAF 305 ******************************************************.89******************** PP TIGR00016 308 kvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvk 384 +++v+Ri+kyig+++ + g+lDaivFt+GiGen+ vr+ v++++++lG+++d++ n rsg+ + i ++ +v lcl|FitnessBrowser__Miya:8501129 306 QMFVYRIRKYIGSFAVVV-GKLDAIVFTAGIGENDDLVRAAVCKDMDILGIDIDEAVNA-KRSGQARHIGKPGQRVP 380 **************9999.66***********************************999.99*************** PP TIGR00016 385 vlviptneelviaeDalr 402 vlv+ptneel ia+ ++ lcl|FitnessBrowser__Miya:8501129 381 VLVVPTNEELEIAQTTVA 398 *************98876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (404 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 10.50 // [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