Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_034525905.1 LOSG293_RS00890 acetate/propionate family kinase
Query= SwissProt::P37877 (395 letters) >NCBI__GCF_000740055.1:WP_034525905.1 Length = 400 Score = 345 bits (884), Expect = 2e-99 Identities = 172/396 (43%), Positives = 263/396 (66%), Gaps = 5/396 (1%) Query: 1 MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60 M K + INAGSSSLK++LF++P+ETV+ +GLVERI + DS+ ++ G K+ E + Sbjct: 1 MKKYLVINAGSSSLKWKLFDIPAETVIAEGLVERINLEDSIVKLAYRGNKSKETVERLSM 60 Query: 61 AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120 + AVK +L L + II L++I +GHR+V G E+F + L I ++ +S+ APL Sbjct: 61 SDAVKSVLRVLVDRKIISRLSDIHAVGHRIVAGAEQFKSATKLDQRAIASLKQLSDYAPL 120 Query: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 180 HNP + ++ LPN P AVFD+ + M +++ L+ +PYE ++F IR+YG HG Sbjct: 121 HNPMQVATVELLATYLPNAPQFAVFDSQLYLQMADETALFGIPYELSKEFHIRRYGEHGI 180 Query: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 240 SH+Y+ + A L+ RPL +L +++ HLG+GAS++A + GK DTSMG TP+ GV MGTRS Sbjct: 181 SHEYLACQTATLMKRPLNELNIVTLHLGSGASVSAFKNGKIYDTSMGLTPVTGVLMGTRS 240 Query: 241 GNIDPALIPYIMEKTG-QTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETA 299 G++DPA++P++M++ +++ VL LN+KSGL G+SG SSD+RD+V + +ERA A Sbjct: 241 GDVDPAIVPFLMKRLQLDSSEAVLALLNEKSGLHGVSGISSDMRDLVAS---DSERANLA 297 Query: 300 LEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNV 359 L++F +++ K IG+Y A M G+DAI F GIGE ++R R++ + +GV DP LN++ Sbjct: 298 LQMFENQVVKQIGAYFAEMGGIDAITFAGGIGEKDSDMRRRIMTRVSHLGVRMDPNLNDL 357 Query: 360 RGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRLAK 395 G E I+ P SP+ +I+PT+EE+ I R V K Sbjct: 358 -GVEGRITIPTSPIMALIVPTNEELAIVRQVAEQLK 392 Lambda K H 0.317 0.136 0.381 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: 373 Number of extensions: 18 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: 395 Length of database: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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_034525905.1 LOSG293_RS00890 (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.591203.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-128 412.5 0.1 9.5e-128 412.3 0.1 1.0 1 NCBI__GCF_000740055.1:WP_034525905.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000740055.1:WP_034525905.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.3 0.1 9.5e-128 9.5e-128 4 401 .. 2 388 .. 1 392 [. 0.96 Alignments for each domain: == domain 1 score: 412.3 bits; conditional E-value: 9.5e-128 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 kk lv+naGssslk++l+d +e+v+++glveri+le++++k g +k++e+++ + + avk +l+ l+ NCBI__GCF_000740055.1:WP_034525905.1 2 KKYLVINAGSSSLKWKLFDIP-AETVIAEGLVERINLEDSIVKLAYRG-NKSKETVERLSMSDAVKSVLRVLV 72 789******************.7*****************77755555.77888899999************* PP TIGR00016 77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149 d+ki+ ls+i+++GHR+v G+e+f++++ +++ +++++k++s++APlHnp ++ ++e + + l++a++ NCBI__GCF_000740055.1:WP_034525905.1 73 -DRKIISRLSDIHAVGHRIVAGAEQFKSATKLDQRAIASLKQLSDYAPLHNPMQVATVELLA--TYLPNAPQF 142 .8*********************************************************999..99******* PP TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222 avFD + +++e++l+++Py+l ke+ +RrYG HG+sh+y++ ++a l+ +pl++ln++++HlG Gasvsa NCBI__GCF_000740055.1:WP_034525905.1 143 AVFDSQLYLQMADETALFGIPYELSKEFHIRRYGEHGISHEYLACQTATLMKRPLNELNIVTLHLGSGASVSA 215 ************************************************************************* PP TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgl.sldeieetlnkksGllgisglssDlRdild 294 knGk +dtsmGltP+ G++mGtRsGd+Dpai+ +l+++l+l s +++ +ln ksGl g+sg+ssD+Rd+++ NCBI__GCF_000740055.1:WP_034525905.1 216 FKNGKIYDTSMGLTPVTGVLMGTRSGDVDPAIVPFLMKRLQLdSSEAVLALLNEKSGLHGVSGISSDMRDLVA 288 ************************************9998763788899**********************98 PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 e+a+lAl+++ + + k ig+y a++ g +Dai F gGiGe ++++r++++ ++ lG+++d++ln NCBI__GCF_000740055.1:WP_034525905.1 289 SD---SERANLALQMFENQVVKQIGAYFAEMGG-IDAITFAGGIGEKDSDMRRRIMTRVSHLGVRMDPNLND- 356 87...6789**********************76.*************************************9. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDal 401 g e+ i+ + s + +l++ptneel+i++ ++ NCBI__GCF_000740055.1:WP_034525905.1 357 --LGVEGRITIPTSPIMALIVPTNEELAIVRQVA 388 ..89999***********************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (400 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: 24.27 // [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