Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_013430189.1 CALKRO_RS06180 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_000166775.1:WP_013430189.1 Length = 399 Score = 490 bits (1261), Expect = e-143 Identities = 236/400 (59%), Positives = 315/400 (78%), Gaps = 1/400 (0%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERELPDHE 60 M+VLV+NSGSSS+KYQ I+ + E LCKG+ +RIG+ G+ + H+ ++ V E+E+ DH Sbjct: 1 MKVLVLNSGSSSLKYQFIDTDTEVALCKGVVDRIGLPGAFIRHQKNGQEIVKEQEINDHN 60 Query: 61 EALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAP 120 A+KL+L L E+ G+I + EIDA+GHRVVHGGE F ++V+V+EEV KAI E LAP Sbjct: 61 VAIKLVLEMLTHEEAGIIHSMDEIDAIGHRVVHGGEYFSDAVIVNEEVKKAIRECIELAP 120 Query: 121 LHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHG 180 LHNPANLMGI+A K +PG PNVAVFDTAFHQT+P+ AY+Y++PYE YEKYKIR+YGFHG Sbjct: 121 LHNPANLMGIEACEKEIPGKPNVAVFDTAFHQTMPRYAYMYSLPYEVYEKYKIRKYGFHG 180 Query: 181 TSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTR 240 TSH+YV+ +AAE L + LEELK+ITCH+GNG+SV A+KYGK VDTSMGFTPL GL MGTR Sbjct: 181 TSHKYVAIKAAEYLRRPLEELKLITCHLGNGSSVCAIKYGKSVDTSMGFTPLAGLAMGTR 240 Query: 241 SGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKL 300 SG +DPA+ ++MEKE + ++M D LNKKSGV G+S G SSD RD+E+AA +G+E +L Sbjct: 241 SGTIDPAVILYLMEKEKMDVKQMNDFLNKKSGVLGIS-GVSSDFRDLEKAANEGNERAQL 299 Query: 301 VLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNE 360 ++++ YR+ KYIG YAA + GVDAI+FTAG+GEN+ + R+ + LE++GV D+++N Sbjct: 300 AIDMFCYRVKKYIGEYAAVLGGVDAIIFTAGIGENNALVRDKCLTDLEYMGVLYDRERNF 359 Query: 361 ETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400 +GK I+ P+S+VKVL+VPTNEELMIAR+TK ++ K Sbjct: 360 NVEKGKVFEINKPESKVKVLIVPTNEELMIARETKRLLSK 399 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: 517 Number of extensions: 24 Number of successful extensions: 2 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: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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 WP_013430189.1 CALKRO_RS06180 (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.2693789.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-171 554.4 0.5 7.4e-171 554.2 0.5 1.0 1 NCBI__GCF_000166775.1:WP_013430189.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430189.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 554.2 0.5 7.4e-171 7.4e-171 4 404 .. 1 397 [. 1 398 [. 0.98 Alignments for each domain: == domain 1 score: 554.2 bits; conditional E-value: 7.4e-171 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 +k+lvln+Gssslk++ +d+ +e l++g+v+ri l++a+i ++++++ ++++i+dh+ a+k +l+ l+ NCBI__GCF_000166775.1:WP_013430189.1 1 MKVLVLNSGSSSLKYQFIDTD-TEVALCKGVVDRIGLPGAFIRH-QKNGQEIVKEQEINDHNVAIKLVLEMLT 71 69*****************99.6999**************8885.5666899999****************** PP TIGR00016 77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 + + i+++++ei++iGHRvvhGge+f+++viv++ev k+i++ +elAPlHnpa+l giea k+++ ++n NCBI__GCF_000166775.1:WP_013430189.1 72 HeEAGIIHSMDEIDAIGHRVVHGGEYFSDAVIVNEEVKKAIRECIELAPLHNPANLMGIEACE--KEIPGKPN 142 98899**********************************************************..999999** PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 vavFDtafHqt+p+ ay+Y+lPy++y+++++R+YGfHGtshkyv+ +aa++l +pl++l+li+cHlGnG+sv+ NCBI__GCF_000166775.1:WP_013430189.1 143 VAVFDTAFHQTMPRYAYMYSLPYEVYEKYKIRKYGFHGTSHKYVAIKAAEYLRRPLEELKLITCHLGNGSSVC 215 ************************************************************************* PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 a+k Gks+dtsmG+tPL+Gl+mGtRsG iDpa+i yl+e++++ ++++++ lnkksG+lgisg+ssD+Rd+++ NCBI__GCF_000166775.1:WP_013430189.1 216 AIKYGKSVDTSMGFTPLAGLAMGTRSGTIDPAVILYLMEKEKMDVKQMNDFLNKKSGVLGISGVSSDFRDLEK 288 ************************************************************************* PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 + +egne+a+lA++++++R++kyig+y+a l g +Dai+Ft+GiGen+a vr+++l +le +G+ d e+n + NCBI__GCF_000166775.1:WP_013430189.1 289 AANEGNERAQLAIDMFCYRVKKYIGEYAAVLGG-VDAIIFTAGIGENNALVRDKCLTDLEYMGVLYDRERNFN 360 *******************************76.**************************************9 PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404 ++gk i+++eskvkvl++ptneel+ia+++ rl NCBI__GCF_000166775.1:WP_013430189.1 361 VEKGKVFEINKPESKVKVLIVPTNEELMIARETKRLL 397 9*******************************99985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (399 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: 20.58 // [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