Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_019615880.1 G327_RS0116355 acetate kinase
Query= BRENDA::E3W769 (401 letters) >NCBI__GCF_000381745.1:WP_019615880.1 Length = 399 Score = 511 bits (1316), Expect = e-149 Identities = 251/400 (62%), Positives = 314/400 (78%), Gaps = 1/400 (0%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 MS+KLVLVLNCGSSSLKFA+I+A +GD+ ISGLAECF L D+R+KW +G K+ A L Sbjct: 1 MSNKLVLVLNCGSSSLKFAVINANNGDEIISGLAECFNLPDARMKWNISGKKDAAHLPPN 60 Query: 61 TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120 +AH EA+ + IV I+ LA Q A+GHR+VHGGEKFT SV+ITP+V + I++CASL Sbjct: 61 SAHAEAISY-IVEEIIKNEQGLAEQFVAVGHRVVHGGEKFTESVVITPDVCKSIKECASL 119 Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180 APLHNPA ++GI+AA A+FP+LPQV VFDTAFHQTMP A++YALPY LY+E IRRYGM Sbjct: 120 APLHNPAAIMGIKAARAAFPELPQVAVFDTAFHQTMPASAFLYALPYHLYKEKGIRRYGM 179 Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240 HGTSH +V REAA++L K + + NVI AHLGNG SV A+K GK VDTSMG+TPL GLVMG Sbjct: 180 HGTSHLFVSREAARLLDKPLAETNVITAHLGNGGSVCAVKNGKCVDTSMGMTPLAGLVMG 239 Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300 TRCGD+DPSII HLV + GY+ V ++L KQSGLLGIS +++D R I+ G++ A Sbjct: 240 TRCGDIDPSIIEHLVAREGYSPAGVMDILQKQSGLLGISGVSSDFRDIQSACEKGNEQAI 299 Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360 LA DIFCYRLAKYIA Y VPLGR+DA++FTGGIGENS ++R+KVLNLL +F ++VD N Sbjct: 300 LARDIFCYRLAKYIAGYAVPLGRIDALVFTGGIGENSAMVRDKVLNLLSVFGYQVDSEKN 359 Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLITA 400 + G++G IT +P AMVIPTNEEWVIA+D+ L++A Sbjct: 360 ETTILGKKGTITTENSPTAMVIPTNEEWVIAQDSASLVSA 399 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: 523 Number of extensions: 28 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: 401 Length of database: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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_019615880.1 G327_RS0116355 (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.3886381.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-163 528.6 0.0 5.2e-163 528.4 0.0 1.0 1 NCBI__GCF_000381745.1:WP_019615880.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_019615880.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 528.4 0.0 5.2e-163 5.2e-163 2 404 .. 2 397 .. 1 398 [. 0.97 Alignments for each domain: == domain 1 score: 528.4 bits; conditional E-value: 5.2e-163 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 ++k++lvln+Gssslkfa+++a+n++++ +sgl+e+++l++ar+k+ +g+k ++ ++h+ea++ ++++ NCBI__GCF_000381745.1:WP_019615880.1 2 SNKLVLVLNCGSSSLKFAVINANNGDEI-ISGLAECFNLPDARMKWNISGKKDAAHLPPNSAHAEAISYIVEE 73 6799********************9998.9******************************************* PP TIGR00016 75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147 + k++ + + ++ ++GHRvvhGgekftesv++t +v k+ik+ ++lAPlHnpa++ gi+a+ ++ + NCBI__GCF_000381745.1:WP_019615880.1 74 IIKNE--QGLAEQFVAVGHRVVHGGEKFTESVVITPDVCKSIKECASLAPLHNPAAIMGIKAAR--AAFPELP 142 *9754..6778899**************************************************..6677889 PP TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220 +vavFDtafHqt+p a+lYalPy+lyke+g+RrYG+HGtsh +v+++aa+ll+kpl++ n+i++HlGnG+sv NCBI__GCF_000381745.1:WP_019615880.1 143 QVAVFDTAFHQTMPASAFLYALPYHLYKEKGIRRYGMHGTSHLFVSREAARLLDKPLAETNVITAHLGNGGSV 215 ************************************************************************* PP TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293 +avknGk++dtsmG+tPL+GlvmGtR+GdiDp+ii +l ++g s + + ++l+k+sGllgisg+ssD+Rdi NCBI__GCF_000381745.1:WP_019615880.1 216 CAVKNGKCVDTSMGMTPLAGLVMGTRCGDIDPSIIEHLVAREGYSPAGVMDILQKQSGLLGISGVSSDFRDIQ 288 ************************************************************************* PP TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366 ++ e+gne+a lA +++++R+akyi+ y+ l g++Da+vFtgGiGen+a+vr++vl+ l v+G ++d+e+n+ NCBI__GCF_000381745.1:WP_019615880.1 289 SACEKGNEQAILARDIFCYRLAKYIAGYAVPL-GRIDALVFTGGIGENSAMVRDKVLNLLSVFGYQVDSEKNE 360 ********************************.67************************************** PP TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDalrla 404 ++ gk++ i+te+s +++viptnee+via+D++ l+ NCBI__GCF_000381745.1:WP_019615880.1 361 TTILGKKGTITTENSP-TAMVIPTNEEWVIAQDSASLV 397 ***********99998.5799************99875 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: 25.82 // [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