Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate N515DRAFT_2456 N515DRAFT_2456 acetate kinase
Query= BRENDA::G4T0C7 (401 letters) >FitnessBrowser__Dyella79:N515DRAFT_2456 Length = 401 Score = 258 bits (658), Expect = 3e-73 Identities = 162/398 (40%), Positives = 223/398 (56%), Gaps = 15/398 (3%) Query: 5 NGNILVINSGSSSIKYRLIA--LPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQS 62 NG IL +N+GSSSIK+ L L ++++ G +E IG E R D ++ + Sbjct: 2 NGIILALNAGSSSIKFALHEHRLAAQRLILRGAIEGIGA-EPRFTAWQPDGAIIDREAWA 60 Query: 63 VIAADHHQAFKAVFEILGEN---CSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRI 119 AA H Q + + + + +GHRVVHGG F P +D + + L + Sbjct: 61 DAAAPHEQLLQPLLAWITARLGAAELAVVGHRVVHGGPSFGQPVRIDTPVMQELERLVSL 120 Query: 120 APLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGF 179 APLH P L + PG+ QVA FDTAFH+ MP A +P Y+D G+RR+GF Sbjct: 121 APLHQPHPLAAARAIARLRPGLMQVACFDTAFHRGMPAVAASLGLPRA-YADDGMRRYGF 179 Query: 180 HGTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMG 239 HG S+ Y+A R EF + D +I HLGNGAS A+ +GRS+DT+MGF+ L+GLVMG Sbjct: 180 HGLSYEYLAGRLREFAPELAD-GRVIMAHLGNGASLCAMRHGRSIDTTMGFSALDGLVMG 238 Query: 240 TRSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTN-DLRTVLEQTNAGDERAR 298 +R G LDP L + Q AI+ L +ESGL G+ G + D+R +L + AR Sbjct: 239 SRCGSLDPGAVLHLLQARGLSVAAIEHLLYQESGLLGVSGISADMRALLASDSG---HAR 295 Query: 299 LALDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAAN 358 A++L+ YRI K IGA +V G +DALVF+ G+GE+AA +R C L+ LG+ DE+AN Sbjct: 296 EAIELFVYRIVKEIGALTSVAGGLDALVFSAGIGEHAASIRSAVCRALAWLGVECDESAN 355 Query: 359 SDVTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVL 396 I+ A S R+ VI+TDEE IA A VL Sbjct: 356 GLHKMLIS---TAHSAVRVFVIRTDEEAVIAAHAAGVL 390 Lambda K H 0.320 0.137 0.400 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: 417 Number of extensions: 18 Number of successful extensions: 6 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: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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 N515DRAFT_2456 N515DRAFT_2456 (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.26424.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-111 358.4 0.0 2.5e-111 358.2 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 N515DRAFT_2456 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 N515DRAFT_2456 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.2 0.0 2.5e-111 2.5e-111 5 400 .. 4 386 .. 1 391 [. 0.92 Alignments for each domain: == domain 1 score: 358.2 bits; conditional E-value: 2.5e-111 TIGR00016 5 kilvlnaGssslkfalldaen.sekvllsglverikleeariktvedge..kkeeeklaiedheea 67 il lnaGsss+kfal +++ +++++l+g +e i e + + dg ++e+ a + he+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 4 IILALNAGSSSIKFALHEHRLaAQRLILRGAIEGIGAEPRFTAWQPDGAiiDREAWADAAAPHEQL 69 69****************9873677799************99999888622334444555667777 PP TIGR00016 68 vkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaeleg 133 ++ ll +++ + +e+a++GHRvvhGg +f + v +++ v+++++++++lAPlH p l + lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 70 LQPLLAWITA----RLGAAELAVVGHRVVHGGPSFGQPVRIDTPVMQELERLVSLAPLHQPHPLAA 131 7777777775....67899*********************************************** PP TIGR00016 134 ieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakl 199 +a+ +l + l +va+FDtafH+ +p a+ +lP ++y + g+RrYGfHG+s++y++ r+ + lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 132 ARAIARLRPGLM--QVACFDTAFHRGMPAVAASLGLP-RAYADDGMRRYGFHGLSYEYLAGRLREF 194 *****7777666..***********************.88999********************998 PP TIGR00016 200 lnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls 265 l+d ++i++HlGnGas++a++ G+sidt+mG+ L+GlvmG+R+G++Dp+++ +l + +gls lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 195 APE-LADGRVIMAHLGNGASLCAMRHGRSIDTTMGFSALDGLVMGSRCGSLDPGAVLHLLQARGLS 259 766.9************************************************************* PP TIGR00016 266 ldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDa 331 +++ie++l ++sGllg+sg+s+D+R +l+ g+ a+ A++++v+Ri k ig+ ++ g lDa lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 260 VAAIEHLLYQESGLLGVSGISADMRALLASD-SGH--AREAIELFVYRIVKEIGALTSVA-GGLDA 321 ***************************9887.566..9*****************98887.55*** PP TIGR00016 332 ivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelvia 397 +vF +GiGe aa++r v+++l+ lG+++d+ n ++ +ist +s+v+v+vi+t+ee via lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 322 LVFSAGIGEHAASIRSAVCRALAWLGVECDESANG----LHKMLISTAHSAVRVFVIRTDEEAVIA 383 *******************************9999....8899**********************9 PP TIGR00016 398 eDa 400 a lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 384 AHA 386 876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (401 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: 00:00:00.01 # Mc/sec: 10.47 // [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