Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_019616529.1 G327_RS0119705 acetate kinase
Query= BRENDA::P63411 (400 letters) >NCBI__GCF_000381745.1:WP_019616529.1 Length = 402 Score = 557 bits (1435), Expect = e-163 Identities = 277/403 (68%), Positives = 329/403 (81%), Gaps = 5/403 (1%) Query: 1 MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60 MS+KL+LVLNCGSSSLKFAIID +GDE +SGLAEC HL +ARIKW ++G K A LG G Sbjct: 1 MSAKLILVLNCGSSSLKFAIIDTTSGDEKISGLAECLHLDDARIKWNLEGVKGSADLGTG 60 Query: 61 AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120 AAH EALN+IV+ +L+QKPEL L AIGHR+VHGGEK+TSSVVI + V++GI++ + A Sbjct: 61 AAHEEALNYIVSELLSQKPELKENLFAIGHRVVHGGEKFTSSVVITDEVMKGIEECVALA 120 Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180 PLHNPAHL+GI A +F L NVAVFDTAFHQTMPEE++LYALPY LY+E GVRRYG Sbjct: 121 PLHNPAHLVGIRAAQHAFASLP--NVAVFDTAFHQTMPEEAFLYALPYKLYRESGVRRYG 178 Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240 HGTSH+Y++ +AA++LNKPV ELNII CHLGNGGSV AI+NG VDTSMG+TPLEGLVM Sbjct: 179 MHGTSHYYISLQAAEVLNKPVNELNIINCHLGNGGSVCAIKNGISVDTSMGMTPLEGLVM 238 Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300 GTR GD+DPA+IFHLHD LG S+++IN MLTKESGLLGLTE TSDCR+VEDNY T AK Sbjct: 239 GTRCGDMDPAVIFHLHDELGYSLEEINTMLTKESGLLGLTEKTSDCRFVEDNYETDTAAK 298 Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360 RAMD+YC+RLAKYI SYTA +DGRLDAVVFTGGIGEN+A +R+L+L +L +LGF+V+ E Sbjct: 299 RAMDLYCYRLAKYIASYTAALDGRLDAVVFTGGIGENSAPIRKLTLERLSLLGFKVNEEA 358 Query: 361 NLAARFGK---SGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400 NLA RFGK G I E + A+VI TNEE VIA D L + Sbjct: 359 NLANRFGKESNQGIITDENSTVAMVIQTNEEWVIAHDTLDLVS 401 Lambda K H 0.318 0.134 0.384 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: 514 Number of extensions: 11 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: 400 Length of database: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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: 50 (23.9 bits)
Align candidate WP_019616529.1 G327_RS0119705 (acetate kinase)
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.4193429.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-171 555.9 0.1 2.7e-171 555.7 0.1 1.0 1 NCBI__GCF_000381745.1:WP_019616529.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_019616529.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 555.7 0.1 2.7e-171 2.7e-171 2 404 .. 2 400 .. 1 401 [. 0.96 Alignments for each domain: == domain 1 score: 555.7 bits; conditional E-value: 2.7e-171 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 + k+ilvln+Gssslkfa++d+++++++ +sgl+e+++l++arik+ +g k++++ ++heea++ ++++ NCBI__GCF_000381745.1:WP_019616529.1 2 SAKLILVLNCGSSSLKFAIIDTTSGDEK-ISGLAECLHLDDARIKWNLEGVKGSADLGTGAAHEEALNYIVSE 73 6789********************9999.9******************************************* PP TIGR00016 75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147 l ++k ++++++ +iGHRvvhGgekft+sv++tdev+k+i++ + lAPlHnpa+l gi+a++ + + + NCBI__GCF_000381745.1:WP_019616529.1 74 LLSQK--PELKENLFAIGHRVVHGGEKFTSSVVITDEVMKGIEECVALAPLHNPAHLVGIRAAQ--HAFASLP 142 **866..9999*****************************************************..6667788 PP TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220 nvavFDtafHqt+peea+lYalPy+ly+e gvRrYG+HGtsh+y++ +aa++lnkp+++ln+i cHlGnG+sv NCBI__GCF_000381745.1:WP_019616529.1 143 NVAVFDTAFHQTMPEEAFLYALPYKLYRESGVRRYGMHGTSHYYISLQAAEVLNKPVNELNIINCHLGNGGSV 215 ************************************************************************* PP TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293 +a+knG s+dtsmG+tPLeGlvmGtR+Gd+Dpa+i++l+++lg sl+ei+++l+k+sGllg+++++sD+R ++ NCBI__GCF_000381745.1:WP_019616529.1 216 CAIKNGISVDTSMGMTPLEGLVMGTRCGDMDPAVIFHLHDELGYSLEEINTMLTKESGLLGLTEKTSDCRFVE 288 ************************************************************************* PP TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366 d++ e++ ak+A+++y++R+akyi++y+a+l+g+lDa+vFtgGiGen+a +r+l+le+l +lG+k+++e n NCBI__GCF_000381745.1:WP_019616529.1 289 DNY-ETDTAAKRAMDLYCYRLAKYIASYTAALDGRLDAVVFTGGIGENSAPIRKLTLERLSLLGFKVNEEANL 360 ***.9999***************************************************************** PP TIGR00016 367 aarsgkes...visteeskvkvlviptneelviaeDalrla 404 a r+gkes +i+ e+s+v ++vi+tnee+via+D+l l+ NCBI__GCF_000381745.1:WP_019616529.1 361 ANRFGKESnqgIITDENSTV-AMVIQTNEEWVIAHDTLDLV 400 99888764332677666665.789************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (402 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: 27.77 // [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