Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_012277819.1 SHAL_RS14195 acetate kinase
Query= BRENDA::E3W769 (401 letters) >NCBI__GCF_000019185.1:WP_012277819.1 Length = 402 Score = 597 bits (1538), Expect = e-175 Identities = 297/402 (73%), Positives = 347/402 (86%), Gaps = 5/402 (1%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAK---- 56 MS+K VLVLNCGSSSLKFA+IDA SG+D +SGL+ECFGLED+ IKWK G+ E+K Sbjct: 1 MSNKYVLVLNCGSSSLKFAVIDAISGEDLLSGLSECFGLEDACIKWKTRVGQQESKHQES 60 Query: 57 LGAFTAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIED 116 LGAF+AH EA+ + IV+ ILA HP L QI A+GHR+VHGGE+F+ SVII EV+QGIE Sbjct: 61 LGAFSAHTEAMAY-IVDTILAAHPTLKQQILAVGHRVVHGGEQFSGSVIINDEVLQGIEA 119 Query: 117 CASLAPLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIR 176 CA+LAPLHNPAH+IGI AA +FPQL Q+ VFDTAFHQTMP+KA+IYALPY+LYREHSIR Sbjct: 120 CATLAPLHNPAHIIGILAAKVAFPQLAQIAVFDTAFHQTMPQKAFIYALPYQLYREHSIR 179 Query: 177 RYGMHGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEG 236 R+GMHGTSH Y+C+ AAK LG V+D+N+I AHLGNGASV AIK G SVDTSMG+TPLEG Sbjct: 180 RFGMHGTSHRYICQTAAKTLGIAVEDLNLISAHLGNGASVTAIKAGISVDTSMGMTPLEG 239 Query: 237 LVMGTRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGH 296 +VMGTRCGDLDPSIIF+LV+ LGY+L EV +++NKQSGLLGISELTNDCRGIEEG+ +GH Sbjct: 240 VVMGTRCGDLDPSIIFYLVQNLGYSLKEVEDMMNKQSGLLGISELTNDCRGIEEGHANGH 299 Query: 297 KGATLALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVD 356 KGA+LALDIFCYRLAKYIASYTVPLGR+DA++FTGGIGENS LIR+KV+ LL IFNFK+D Sbjct: 300 KGASLALDIFCYRLAKYIASYTVPLGRIDALVFTGGIGENSALIRQKVIELLSIFNFKLD 359 Query: 357 DILNKAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398 N AARFGQQG IT P+AMVIPTNEEWVIA+DA+KLI Sbjct: 360 RQRNLAARFGQQGQITADTGPVAMVIPTNEEWVIAQDALKLI 401 Lambda K H 0.321 0.139 0.409 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: 546 Number of extensions: 21 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: 401 Length of database: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_012277819.1 SHAL_RS14195 (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.497354.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-160 519.2 0.1 3.5e-160 519.1 0.1 1.0 1 NCBI__GCF_000019185.1:WP_012277819.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019185.1:WP_012277819.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 519.1 0.1 3.5e-160 3.5e-160 2 404 .. 2 401 .. 1 402 [] 0.95 Alignments for each domain: == domain 1 score: 519.1 bits; conditional E-value: 3.5e-160 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktv....edgekkeeeklaiedheeavkk 70 ++k +lvln+Gssslkfa++da ++e + lsgl e++ le+a ik++ ++++k++e a+++h+ea++ NCBI__GCF_000019185.1:WP_012277819.1 2 SNKYVLVLNCGSSSLKFAVIDAISGEDL-LSGLSECFGLEDACIKWKtrvgQQESKHQESLGAFSAHTEAMAY 73 6789*******************87776.9****************942222334456677899********* PP TIGR00016 71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143 +++t+ + + +++++i ++GHRvvhGge+f+ svi++devl++i+ + lAPlHnpa+++gi a++ ++ NCBI__GCF_000019185.1:WP_012277819.1 74 IVDTILA--AHPTLKQQILAVGHRVVHGGEQFSGSVIINDEVLQGIEACATLAPLHNPAHIIGILAAKVAF-- 142 ******7..559999*****************************************************555.. PP TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216 ++ ++avFDtafHqt+p++a++YalPy+ly+e+ +Rr+G+HGtsh+y+ q+aak+l+ +++dlnli++HlGn NCBI__GCF_000019185.1:WP_012277819.1 143 PQLAQIAVFDTAFHQTMPQKAFIYALPYQLYREHSIRRFGMHGTSHRYICQTAAKTLGIAVEDLNLISAHLGN 215 5556********************************************************************* PP TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289 Gasv+a+k G s+dtsmG+tPLeG+vmGtR+Gd+Dp+ii+yl ++lg sl+e+e+++nk+sGllgis+l++D+ NCBI__GCF_000019185.1:WP_012277819.1 216 GASVTAIKAGISVDTSMGMTPLEGVVMGTRCGDLDPSIIFYLVQNLGYSLKEVEDMMNKQSGLLGISELTNDC 288 ************************************************************************* PP TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362 R i++ ++g++ a+lAl+++++R+akyi++y+ l g++Da+vFtgGiGen+a +r++v+e l ++ +kld NCBI__GCF_000019185.1:WP_012277819.1 289 RGIEEGHANGHKGASLALDIFCYRLAKYIASYTVPL-GRIDALVFTGGIGENSALIRQKVIELLSIFNFKLDR 360 ************************************.67********************************** PP TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404 ++n aar+g+++ i+ + + v ++viptnee+via+Dal+l+ NCBI__GCF_000019185.1:WP_012277819.1 361 QRNLAARFGQQGQITADTGPV-AMVIPTNEEWVIAQDALKLI 401 ***************777766.789**************996 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: 25.59 // [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