Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_090447849.1 BLS63_RS21520 acetate kinase
Query= BRENDA::E3W769 (401 letters) >NCBI__GCF_900100495.1:WP_090447849.1 Length = 394 Score = 385 bits (988), Expect = e-111 Identities = 199/398 (50%), Positives = 264/398 (66%), Gaps = 5/398 (1%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 M + +LV+NCGSSS+KFA+++ +SGLAE G D+ + W+ GG+ ++ + A Sbjct: 1 MPARNILVINCGSSSIKFALVNEAHSQFTLSGLAERLGSHDAVLHWQ-RGGERDSLMIAN 59 Query: 61 TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120 HR A + + Q+ IGHR+VHGGE FT + + +Q I A L Sbjct: 60 ADHRAA----LAQLLPLVQAAAGGQLHGIGHRVVHGGEHFTAASRLDEAALQAIRATAPL 115 Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180 APLHNPA+L+GI AAI FP+LPQV VFDTAFHQT+PE A+ YALP LYREH +RRYG Sbjct: 116 APLHNPANLLGIEAAIKLFPKLPQVAVFDTAFHQTLPEHAFRYALPDSLYREHGVRRYGF 175 Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240 HGTSH +V AA++ G V D + + AHLGNG S AI+GG+S DTSMGLTPLEGLVMG Sbjct: 176 HGTSHRFVSHRAAELAGLAVGDSSWLVAHLGNGCSTCAIEGGQSRDTSMGLTPLEGLVMG 235 Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300 TR GD+DP++ HL + LG+ L+ + LLN++SGLLG+S L+ND R +E+ GH GAT Sbjct: 236 TRSGDVDPNLHSHLARTLGWNLERIERLLNQESGLLGLSGLSNDMRSLEQAREQGHAGAT 295 Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360 LA+++FCYRLAK +A+ + L +LD ++FTGGIGENS LIR K + L++ N +D N Sbjct: 296 LAIEVFCYRLAKSLAAMSCALSQLDGLVFTGGIGENSPLIRSKTVAHLKLLNLALDKQAN 355 Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398 G G I G P +V+PTNEE IA D + L+ Sbjct: 356 ARTIRGVGGAIHAHGHPRVLVVPTNEERQIALDTLALL 393 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: 490 Number of extensions: 27 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: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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_090447849.1 BLS63_RS21520 (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.231398.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-139 451.5 0.0 1.3e-139 451.4 0.0 1.0 1 NCBI__GCF_900100495.1:WP_090447849.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100495.1:WP_090447849.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.4 0.0 1.3e-139 1.3e-139 4 403 .. 4 392 .. 1 394 [] 0.96 Alignments for each domain: == domain 1 score: 451.4 bits; conditional E-value: 1.3e-139 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 + ilv+n+Gsss+kfal++ ++ ++ lsgl+er+ +++a++ + + g+++++ + a +dh++a+++ll ++ NCBI__GCF_900100495.1:WP_090447849.1 4 RNILVINCGSSSIKFALVNEAH-SQFTLSGLAERLGSHDAVLHW-QRGGERDSLMIANADHRAALAQLLPLVQ 74 689*****************96.56669************6665.66778899999*************9998 PP TIGR00016 77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149 + +++ iGHRvvhGge+ft + +++ +l++i+ ++lAPlHnpa+l giea+ k +k ++v NCBI__GCF_900100495.1:WP_090447849.1 75 A-----AAGGQLHGIGHRVVHGGEHFTAASRLDEAALQAIRATAPLAPLHNPANLLGIEAAI--KLFPKLPQV 140 4.....78899***************************************************..6667888** PP TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222 avFDtafHqt+pe+a+ YalP sly+e+gvRrYGfHGtsh++v++raa+l + ++ d+ +v+HlGnG s +a NCBI__GCF_900100495.1:WP_090447849.1 141 AVFDTAFHQTLPEHAFRYALPDSLYREHGVRRYGFHGTSHRFVSHRAAELAGLAVGDSSWLVAHLGNGCSTCA 213 ************************************************************************* PP TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295 ++ G+s dtsmGltPLeGlvmGtRsGd+Dp + s+la tlg l+ ie++ln++sGllg+sgls+D+R ++++ NCBI__GCF_900100495.1:WP_090447849.1 214 IEGGQSRDTSMGLTPLEGLVMGTRSGDVDPNLHSHLARTLGWNLERIERLLNQESGLLGLSGLSNDMRSLEQA 286 ************************************************************************* PP TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368 e+g+ a+lA++v+++R+ak ++++ +l++ lD++vFtgGiGen+ +r +++ +l++l l+ld++ n ++ NCBI__GCF_900100495.1:WP_090447849.1 287 REQGHAGATLAIEVFCYRLAKSLAAMSCALSQ-LDGLVFTGGIGENSPLIRSKTVAHLKLLNLALDKQANART 358 ******************************77.**************************************** PP TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrl 403 +g + i +++ +vlv+ptnee ia D+l l NCBI__GCF_900100495.1:WP_090447849.1 359 IRGVGGAIH-AHGHPRVLVVPTNEERQIALDTLAL 392 999999997.8999*****************9877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (394 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13.38 // [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