Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_062735420.1 AYX06_RS08595 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_001580365.1:WP_062735420.1 Length = 380 Score = 343 bits (881), Expect = 4e-99 Identities = 187/403 (46%), Positives = 257/403 (63%), Gaps = 30/403 (7%) Query: 1 MRVLVINSGSSSIKYQLIEME----GEKVLCKGIAERIGIEGSRLVHRVGDEKHVIEREL 56 M VLV+N GSSS+KYQ+ E+E G VL G+ E IG + Sbjct: 1 MLVLVVNCGSSSLKYQVRELEPGADGGTVLTSGLIENIG-----------------SSRI 43 Query: 57 PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116 DH +AL+L+ L E G + +DA GHRVVHGGERF VL E+++ IE + Sbjct: 44 QDHTQALELLAGRLETELDG-----RTVDAAGHRVVHGGERFSAPVLATPEIIRDIERLV 98 Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176 PLAPLHNPA ++G++A K P +P V VFDTAFH+T+P+ + YA+P +YE + IRRY Sbjct: 99 PLAPLHNPAAVLGLRAVQKTWPHLPQVCVFDTAFHRTMPEHVWRYAVPERFYEHWGIRRY 158 Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236 GFHGTSH +V+ +AAE LG E + + H+GNGASV A++ G+ DTSMG+TPL GLV Sbjct: 159 GFHGTSHDWVTGQAAEFLGIPRERFRAVVAHLGNGASVTAIRDGRSYDTSMGYTPLAGLV 218 Query: 237 MGTRSGDLDPAIPFFIMEKE-GISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295 MGTR+GDLDP++ ++ ++ ++P+ + +LNK+SG+ ++ DMR ++EAA +GD Sbjct: 219 MGTRTGDLDPSVVTAVLRRDPEMTPERLDAVLNKESGLRAVAG--DHDMRAVQEAAERGD 276 Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355 E +L LE+ YR+AKY+G Y A+ G A+VFTAG+GEN+ R+ VC L LGV+LD Sbjct: 277 ERAELALEMAAYRLAKYVGGYHVAVEGAQALVFTAGIGENAAPFRKRVCDRLGALGVRLD 336 Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398 N RG IS P S ++VLVVPT+EE IA T +V Sbjct: 337 DDANAARARGTRR-ISAPGSALEVLVVPTDEEQAIAAATAALV 378 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: 391 Number of extensions: 16 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: 403 Length of database: 380 Length adjustment: 31 Effective length of query: 372 Effective length of database: 349 Effective search space: 129828 Effective search space used: 129828 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_062735420.1 AYX06_RS08595 (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.585991.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-126 408.2 0.0 1.4e-124 401.9 0.0 2.0 1 NCBI__GCF_001580365.1:WP_062735420.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001580365.1:WP_062735420.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.9 0.0 1.4e-124 1.4e-124 4 403 .. 1 377 [. 1 379 [. 0.95 Alignments for each domain: == domain 1 score: 401.9 bits; conditional E-value: 1.4e-124 TIGR00016 4 kkilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 +++lv+n+Gssslk+++ + e + +vl+sgl+e+i ++ i+dh++a++ l+ NCBI__GCF_001580365.1:WP_062735420.1 1 MLVLVVNCGSSSLKYQVRELEPgadGGTVLTSGLIENIGSSR------------------IQDHTQALELLAG 55 579**************9998544478899999999987654..................479********** PP TIGR00016 74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146 +l++ + +++ GHRvvhGge+f+ v+ t e++++i+++++lAPlHnpa++ g++av+ k+ ++ NCBI__GCF_001580365.1:WP_062735420.1 56 RLET----ELDGRTVDAAGHRVVHGGERFSAPVLATPEIIRDIERLVPLAPLHNPAAVLGLRAVQ--KTWPHL 122 ***8....457889***************************************************..889999 PP TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219 ++v vFDtafH+t+pe+ + Ya+P+++y++ g+RrYGfHGtsh +vt +aa+ l+ p + + +v+HlGnGas NCBI__GCF_001580365.1:WP_062735420.1 123 PQVCVFDTAFHRTMPEHVWRYAVPERFYEHWGIRRYGFHGTSHDWVTGQAAEFLGIPRERFRAVVAHLGNGAS 195 9************************************************************************ PP TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisyl.aetlglsldeieetlnkksGllgisglssDlRd 291 v+a+++G+s+dtsmG tPL+GlvmGtR+Gd+Dp++++ + +++ + + +lnk+sGl +++g D+R NCBI__GCF_001580365.1:WP_062735420.1 196 VTAIRDGRSYDTSMGYTPLAGLVMGTRTGDLDPSVVTAVlRRDPEMTPERLDAVLNKESGLRAVAG-DHDMRA 267 ***********************************9876156779*********************.9***** PP TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364 + ++ e g+e+a+lAl++ ++R+aky+g y ++eg a+vFt+GiGenaa r++v+++l lG++ld + NCBI__GCF_001580365.1:WP_062735420.1 268 VQEAAERGDERAELALEMAAYRLAKYVGGYHVAVEG-AQALVFTAGIGENAAPFRKRVCDRLGALGVRLDDDA 339 **********************************99.9*********************************** PP TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalrl 403 n ar + is + s+++vlv+pt+ee +ia ++ l NCBI__GCF_001580365.1:WP_062735420.1 340 NA-ARARGTRRISAPGSALEVLVVPTDEEQAIAAATAAL 377 99.9999999**********************9877665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (380 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.64 // [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