Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_062055201.1 N456_RS06675 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_001401755.1:WP_062055201.1 Length = 394 Score = 407 bits (1046), Expect = e-118 Identities = 216/397 (54%), Positives = 292/397 (73%), Gaps = 11/397 (2%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERE--LPD 58 M+VLV+NSGSSSIK+QL M KV+C G+ ERIG++ +++ ++ E+ IE+E + + Sbjct: 1 MQVLVLNSGSSSIKFQLFTMPEAKVICSGMVERIGLDNAKIKYQ--SEQIAIEKEEDIKN 58 Query: 59 HEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPL 118 H++ L+LI N L+D+K+GV++ +I VGHRVVHGG F ++V V EEV + I+E+S L Sbjct: 59 HKDGLQLIANYLMDDKIGVLQSASDISIVGHRVVHGGNTFAKTVEVTEEVKRKIKELSSL 118 Query: 119 APLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGF 178 APLHNPANL GI A ++ VAVFDTAFHQTIP +A+ YAIP + EK+ IR YGF Sbjct: 119 APLHNPANLEGIIVAEEIFSQANQVAVFDTAFHQTIPVEAHKYAIPNTFLEKHNIRVYGF 178 Query: 179 HGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMG 238 HGTSH+YVS++A + LG +++ KIIT H+GNG S+ AVK GK +D ++GF P+ GL+MG Sbjct: 179 HGTSHKYVSEKAIDFLG--IQQSKIITIHLGNGCSMTAVKNGKSIDHTLGFAPMNGLIMG 236 Query: 239 TRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWC 298 TR GD+DPAI F+++ G S +E+ +L K+SG+ GL+ G+ SD+RDIE A KG+ C Sbjct: 237 TRCGDIDPAILFYMVNTLGYSLEEVNMLLQKESGMLGLT-GY-SDLRDIEAQAEKGNTDC 294 Query: 299 KLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQK 358 KL LE+ YRI KYIG+YA +NG+DAIVFTAG+GENS + R VC L+FLG++LD +K Sbjct: 295 KLALEMNAYRIKKYIGSYATILNGLDAIVFTAGIGENSDLMRSLVCENLDFLGIELDTEK 354 Query: 359 NEETIRGKE-GIISTPDSRVKVLVVPTNEELMIARDT 394 N IR KE IS P SRVKVLV+PTNEEL IA+ + Sbjct: 355 NR--IRSKETRTISLPSSRVKVLVIPTNEELEIAKQS 389 Lambda K H 0.318 0.138 0.391 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: 423 Number of extensions: 11 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: 403 Length of database: 394 Length adjustment: 31 Effective length of query: 372 Effective length of database: 363 Effective search space: 135036 Effective search space used: 135036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_062055201.1 N456_RS06675 (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.70555.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-150 485.7 5.6 5.4e-150 485.5 5.6 1.0 1 NCBI__GCF_001401755.1:WP_062055201.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001401755.1:WP_062055201.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.5 5.6 5.4e-150 5.4e-150 4 401 .. 1 390 [. 1 394 [] 0.96 Alignments for each domain: == domain 1 score: 485.5 bits; conditional E-value: 5.4e-150 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 +++lvln+Gsss+kf+l+ + + kv++sg+veri l++a+ik ++++ e++ +i++h+ +++ ++n l+ NCBI__GCF_001401755.1:WP_062055201.1 1 MQVLVLNSGSSSIKFQLFTMPE-AKVICSGMVERIGLDNAKIK-YQSEQIAIEKEEDIKNHKDGLQLIANYLM 71 579******************7.6677*************877.455567888999***************** PP TIGR00016 77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 + + +l++ s+i+++GHRvvhGg++f+++v vt+ev +kik++s+lAPlHnpa+legi + ++ +a++ NCBI__GCF_001401755.1:WP_062055201.1 72 DdKIGVLQSASDISIVGHRVVHGGNTFAKTVEVTEEVKRKIKELSSLAPLHNPANLEGIIVAE--EIFSQANQ 142 867789*****************************************************9999..7778888* PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 vavFDtafHqtip ea+ Ya+P + +++++R YGfHGtshkyv+++a + l+ +++++i++HlGnG s++ NCBI__GCF_001401755.1:WP_062055201.1 143 VAVFDTAFHQTIPVEAHKYAIPNTFLEKHNIRVYGFHGTSHKYVSEKAIDFLGI--QQSKIITIHLGNGCSMT 213 ****************************************************98..9**************** PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 avknGksid ++G+ P++Gl+mGtR+GdiDpai++y+ +tlg sl+e++ +l+k+sG+lg++g sDlRdi++ NCBI__GCF_001401755.1:WP_062055201.1 214 AVKNGKSIDHTLGFAPMNGLIMGTRCGDIDPAILFYMVNTLGYSLEEVNMLLQKESGMLGLTG-YSDLRDIEA 285 ***************************************************************.89******* PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 + e+gn ++klAl++ ++Ri+kyig+y++ l+g lDaivFt+GiGen+ +r lv+e+l++lG++ld+e+n NCBI__GCF_001401755.1:WP_062055201.1 286 QAEKGNTDCKLALEMNAYRIKKYIGSYATILNG-LDAIVFTAGIGENSDLMRSLVCENLDFLGIELDTEKNR- 356 *******************************88.*************************************9. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDal 401 rs++ + is + s+vkvlviptneel ia+ ++ NCBI__GCF_001401755.1:WP_062055201.1 357 IRSKETRTISLPSSRVKVLVIPTNEELEIAKQSF 390 899999************************9876 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 21.04 // [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