Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate GFF1535 HP15_1499 acetate/propionate kinase
Query= BRENDA::E3W769 (401 letters) >FitnessBrowser__Marino:GFF1535 Length = 398 Score = 349 bits (896), Expect = e-101 Identities = 189/393 (48%), Positives = 255/393 (64%), Gaps = 7/393 (1%) Query: 6 VLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAFTAHRE 65 VLV+NCGSSSLK A+ + Q +S LAE G D+ +G + L A H + Sbjct: 5 VLVVNCGSSSLKLALFNNQHRK-LVSALAERLGQSDAFAH--IDGQEGTIPLDAGAGHDQ 61 Query: 66 AVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASLAPLHN 125 A+E + + + AIGHR+VHGGE F +V+I +V++ IE CA LAPLHN Sbjct: 62 ALETLVT--AFRDLGLMTTAPSAIGHRVVHGGETFHEAVLIDGDVLKAIESCAGLAPLHN 119 Query: 126 PAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGMHGTSH 185 P +L GIRA +A FP +PQ VFDTAFHQT+P +A++YALP YR+ IRRYG HGTSH Sbjct: 120 PVNLSGIRATLAQFPDVPQTAVFDTAFHQTLPRRAFLYALPEAWYRDWGIRRYGFHGTSH 179 Query: 186 FYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMGTRCGD 245 ++ EAA++LGK +VI AHLGNG S+ AI+ G SVDTSMGLTPLEGLVMGTR GD Sbjct: 180 AFMASEAARLLGKTPATTSVISAHLGNGCSITAIRDGISVDTSMGLTPLEGLVMGTRSGD 239 Query: 246 LDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGATLALDI 305 +DP +F ++ G DEV+ +LN++SGLLG+S TND R + E GH+ + A+D+ Sbjct: 240 VDPG-LFDFLRSKGIAADEVHRVLNQESGLLGLSGQTNDMRSLCELADHGHEPSQTAIDV 298 Query: 306 FCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN-KAAR 364 FC+RLA+Y+ + L +LDA++FTGGIGENS IRE+ + L++ F++ LN + Sbjct: 299 FCFRLARYVGAMMASLSQLDALVFTGGIGENSPRIREETIRHLKLTGFELSQDLNIHHGQ 358 Query: 365 FGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKL 397 F + + +VIPTNEE VIA +A +L Sbjct: 359 FSDGHIESPDSRFPVLVIPTNEELVIAREATRL 391 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: 425 Number of extensions: 20 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: 401 Length of database: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 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 GFF1535 HP15_1499 (acetate/propionate 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.4414.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-143 464.4 0.0 1.6e-143 464.2 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1535 HP15_1499 acetate/propionate kin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1535 HP15_1499 acetate/propionate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 464.2 0.0 1.6e-143 1.6e-143 4 404 .. 3 392 .. 1 393 [. 0.97 Alignments for each domain: == domain 1 score: 464.2 bits; conditional E-value: 1.6e-143 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 +lv+n+Gssslk al++++ +++l+s+l+er+ ++a + dg++++ a + h++a+++l++++ d lcl|FitnessBrowser__Marino:GFF1535 3 DTVLVVNCGSSSLKLALFNNQ--HRKLVSALAERLGQSDA--FAHIDGQEGTIPLDAGAGHDQALETLVTAFR-D 72 679****************99..68889********9999..677999999999******************9.6 PP TIGR00016 79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFD 153 ++++ ++iGHRvvhGge+f e+v+++ +vlk+i+ + lAPlHnp +l+gi+a l + +++++ avFD lcl|FitnessBrowser__Marino:GFF1535 73 LGLMTTAP--SAIGHRVVHGGETFHEAVLIDGDVLKAIESCAGLAPLHNPVNLSGIRATL--AQFPDVPQTAVFD 143 77776655..69**********************************************99..888999******* PP TIGR00016 154 tafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGks 228 tafHqt+p++a+lYalP+ +y++ g+RrYGfHGtsh +++ +aa+ll+k+ + +i++HlGnG s++a+++G s lcl|FitnessBrowser__Marino:GFF1535 144 TAFHQTLPRRAFLYALPEAWYRDWGIRRYGFHGTSHAFMASEAARLLGKTPATTSVISAHLGNGCSITAIRDGIS 218 *************************************************************************** PP TIGR00016 229 idtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneea 303 +dtsmGltPLeGlvmGtRsGd+Dp++ +l + +g ++de++++ln++sGllg+sg ++D+R + + ++g+e + lcl|FitnessBrowser__Marino:GFF1535 219 VDTSMGLTPLEGLVMGTRSGDVDPGLFDFLRS-KGIAADEVHRVLNQESGLLGLSGQTNDMRSLCELADHGHEPS 292 *****************************986.699*************************************** PP TIGR00016 304 klAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvist 378 ++A++v++ R+a+y+g+++asl++ lDa+vFtgGiGen+ +re+++++l++ G++l ++ln + + +++ i + lcl|FitnessBrowser__Marino:GFF1535 293 QTAIDVFCFRLARYVGAMMASLSQ-LDALVFTGGIGENSPRIREETIRHLKLTGFELSQDLNIHHGQFSDGHIES 366 **********************77.**************************************999********* PP TIGR00016 379 eeskvkvlviptneelviaeDalrla 404 ++s++ vlviptneelvia++a+rla lcl|FitnessBrowser__Marino:GFF1535 367 PDSRFPVLVIPTNEELVIAREATRLA 392 **********************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (398 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: 00:00:00.02 # Mc/sec: 6.90 // [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