Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate WP_061533398.1 CAter10_RS10715 acetate/propionate family kinase
Query= SwissProt::P74879 (404 letters) >NCBI__GCF_001584165.1:WP_061533398.1 Length = 406 Score = 258 bits (658), Expect = 3e-73 Identities = 163/395 (41%), Positives = 223/395 (56%), Gaps = 13/395 (3%) Query: 5 IMAINAGSSSLKFQLLEMPQGDMLCQ----GLIERIGMADAQVTIKTHSQKWQETVPVAD 60 I+ +N GSSS+KF L + + Q G ++ IG + + T S V Sbjct: 14 ILVLNCGSSSIKFALFDTSPAVLARQADWKGKVDGIGGKPSYIESGTESAPLALGT-VQP 72 Query: 61 HRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAELAP 120 + DA+ + E++ + R + V HRV HGG + T + E LA ++ LAP Sbjct: 73 YHDALMHIRERVALHL---GARRLCAVAHRVVHGGSKYSAPTRIDAEVLADLKNYIPLAP 129 Query: 121 LHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGFHG 180 LH P I V P VA FDTAFH TL + PLP H E G+RRYGFHG Sbjct: 130 LHQPFALEAIEVLLSSQPGLLQVACFDTAFHHTLPHVEQMLPLP-HALWERGLRRYGFHG 188 Query: 181 TSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMGTR 240 S++Y+S VL E+ G S RVI HLG+G+S+CA++ RSV T+MGF+ G+MMGTR Sbjct: 189 LSYEYMSVVLEERFGAA-SHGRVIAAHLGSGASLCAMRALRSVGTTMGFSALDGLMMGTR 247 Query: 241 SGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDV---EQAANTGNRQA 297 G +DP + ++ + E + +Q+ LL +ESGLLGVSG SSD + EQ + + Sbjct: 248 CGALDPGAVLYLMEIEKLSLEQVAHLLYHESGLLGVSGFSSDPPVLFAQEQRQDAVGDRV 307 Query: 298 KLALTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEK 357 + AL L+ RI IG+ +GGLD LVFT GIGE+SA RS VC +L FLG+ +D+E Sbjct: 308 RAALDLYVRRIVREIGALAAVLGGLDLLVFTAGIGEHSAEIRSRVCRDLAFLGVGLDQES 367 Query: 358 NQRNATFIQTENALVKVAVINTNEELMIAQDVMRI 392 NQRNA FI ++ V VAV TNEE + A+ + I Sbjct: 368 NQRNAPFISLVDSRVTVAVEPTNEEWIAARHTLAI 402 Lambda K H 0.319 0.135 0.392 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: 355 Number of extensions: 20 Number of successful extensions: 5 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: 404 Length of database: 406 Length adjustment: 31 Effective length of query: 373 Effective length of database: 375 Effective search space: 139875 Effective search space used: 139875 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_061533398.1 CAter10_RS10715 (acetate/propionate family 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.3864870.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-106 339.8 0.0 1.2e-105 339.5 0.0 1.0 1 NCBI__GCF_001584165.1:WP_061533398.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001584165.1:WP_061533398.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.5 0.0 1.2e-105 1.2e-105 5 401 .. 13 400 .. 10 404 .. 0.91 Alignments for each domain: == domain 1 score: 339.5 bits; conditional E-value: 1.2e-105 TIGR00016 5 kilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 ilvln+Gsss+kfal+d++ +++ ++g v+ i + + i + +e + ++ ++ a+ ++ ++ NCBI__GCF_001584165.1:WP_061533398.1 13 FILVLNCGSSSIKFALFDTSPavlARQADWKGKVDGIGGKPSYIE--SGTESAPLALGTVQPYHDALMHIRER 83 59****************997555667789*******99999554..444456677888999*******9999 PP TIGR00016 75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147 + ++ + ++ HRvvhGg+k++ + +++evl+++k+ ++lAPlH p +le+ie +l ++ NCBI__GCF_001584165.1:WP_061533398.1 84 VA----LHLGARRLCAVAHRVVHGGSKYSAPTRIDAEVLADLKNYIPLAPLHQPFALEAIEVLL--SSQPGLL 150 98....466788999*************************************************..5566666 PP TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220 +va+FDtafH+t+p+ + +lP+ l++ g+RrYGfHG+s++y++ +++ ++ + + ++i +HlG Gas+ NCBI__GCF_001584165.1:WP_061533398.1 151 QVACFDTAFHHTLPHVEQMLPLPHALWE-RGLRRYGFHGLSYEYMSVVLEERFGA-ASHGRVIAAHLGSGASL 221 ***********************88885.79***********************9.7899************* PP TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293 +a++ +s+ t+mG+ L+Gl+mGtR+G +Dp+++ yl+e ++lsl+++ ++l +sGllg+sg+ssD +++ NCBI__GCF_001584165.1:WP_061533398.1 222 CAMRALRSVGTTMGFSALDGLMMGTRCGALDPGAVLYLMEIEKLSLEQVAHLLYHESGLLGVSGFSSDPPVLF 294 ********************************************************************99988 PP TIGR00016 294 dkke...egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldle 363 ++ + + ++ + Al++yv Ri + ig+ +a l g lD +vFt+GiGe +ae+r +v+++l++lG+ ld+e NCBI__GCF_001584165.1:WP_061533398.1 295 AQEQrqdAVGDRVRAALDLYVRRIVREIGALAAVLGG-LDLLVFTAGIGEHSAEIRSRVCRDLAFLGVGLDQE 366 766521145578999********************76.*********************************** PP TIGR00016 364 lnnaarsgkesvisteeskvkvlviptneelviaeDal 401 n+ + +is +s+v+v+v ptnee++ a+ +l NCBI__GCF_001584165.1:WP_061533398.1 367 SNQ----RNAPFISLVDSRVTVAVEPTNEEWIAARHTL 400 *99....7789********************9998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (406 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: 17.50 // [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