Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate 209544 DVU0600 L-lactate dehydrogenase
Query= BRENDA::B1A4R6 (311 letters) >MicrobesOnline__882:209544 Length = 309 Score = 286 bits (733), Expect = 3e-82 Identities = 139/302 (46%), Positives = 210/302 (69%) Query: 1 MSKISVIGSGFVGATTAYTLALSGIAKTIVLIDINKDKAEGDALDISHGVPFISPVEVYA 60 M++I+VIG G VG AY A+ +A IVLID N +AEG+++D++ + + PV++ + Sbjct: 1 MNRIAVIGVGNVGMAFAYAAAIKRLANDIVLIDANAARAEGESMDLADAMALVGPVQIRS 60 Query: 61 GDYGDTVGSDIIIITAGAAQKPGETRLDLVKKNTMIFKDIVAKLIKVNDTAIYLIVTNPV 120 G Y G+ I+++TAGA Q PG++RLDLV+ N I +DI+ +++ D +Y++ TNPV Sbjct: 61 GGYEQCEGARIVVVTAGAKQMPGQSRLDLVRVNAGITRDILTAVMQYADDPLYIMATNPV 120 Query: 121 DILTYVTYKISGLPYGRVLGSGTVLDSARFRYLLSKHCNIDPRNIHGYIIGEHGDSELAA 180 D+LT+V ++G+ GRV+GSGTVLDSARFR +++ +D R +H +I+GEHGDSE+A Sbjct: 121 DVLTHVARTVTGVAPGRVIGSGTVLDSARFRGHVAEILGVDVRGVHAHIVGEHGDSEVAL 180 Query: 181 WSITNIAGIPIDNYCNLCGKVCEKDFREEIFNNVVRAAYTIIEKKGATYYAVALAVRRIV 240 WS N++GIP+ C G + FRE+ +V AAY II +KGAT Y + +++ RIV Sbjct: 181 WSRANVSGIPVAEMCARRGIAYDAAFREKALGHVRHAAYEIIGRKGATGYGIGMSLCRIV 240 Query: 241 EAILRDENSILTVSSPLTGQYGVTDVALSLPSVVGRNGIVNILELPLSQEEIAAFRRSAE 300 EAIL DE+S+LTVS P+ G YG+ DV+LSLP V+G +GI +L+ P++++E AA SA Sbjct: 241 EAILHDEHSVLTVSCPVAGHYGLGDVSLSLPCVIGSDGIEEVLDAPIAEDEQAALAASAR 300 Query: 301 II 302 ++ Sbjct: 301 VL 302 Lambda K H 0.319 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: 280 Number of extensions: 6 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: 311 Length of database: 309 Length adjustment: 27 Effective length of query: 284 Effective length of database: 282 Effective search space: 80088 Effective search space used: 80088 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: 48 (23.1 bits)
Align candidate 209544 DVU0600 (L-lactate dehydrogenase)
to HMM TIGR01771 (L-lactate dehydrogenase (EC 1.1.1.27))
# 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/TIGR01771.hmm # target sequence database: /tmp/gapView.6565.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01771 [M=299] Accession: TIGR01771 Description: L-LDH-NAD: L-lactate dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-109 349.6 0.3 8.9e-109 349.4 0.3 1.0 1 lcl|MicrobesOnline__882:209544 DVU0600 L-lactate dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209544 DVU0600 L-lactate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.4 0.3 8.9e-109 8.9e-109 1 297 [. 6 302 .. 6 304 .. 0.99 Alignments for each domain: == domain 1 score: 349.4 bits; conditional E-value: 8.9e-109 TIGR01771 1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvitaGaeqkpg 79 +iG+g+VG+++a+a++ + la+++vliD n +aege +dl+da++++ +v++++g ye++++a++vv+taGa+q pg lcl|MicrobesOnline__882:209544 6 VIGVGNVGMAFAYAAAIKRLANDIVLIDANAARAEGESMDLADAMALV-GPVQIRSGGYEQCEGARIVVVTAGAKQMPG 83 8**********************************************9.88**************************** PP TIGR01771 80 etRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdtaRlrrllaeklevdp 158 ++Rl+lv+ n+ i ++i++ v++++ d ++++++NPvD+lt+v+++++g+ + rviGsGtvLd+aR+r ++ae l+vd lcl|MicrobesOnline__882:209544 84 QSRLDLVRVNAGITRDILTAVMQYADDPLYIMATNPVDVLTHVARTVTGVAPGRVIGSGTVLDSARFRGHVAEILGVDV 162 ******************************************************************************* PP TIGR01771 159 ksvhayvlGEHGdsevavwssakiagvplkelleekekekekelk.eiekevrdaayeiiekKgaTsygiglavarive 236 + vha+++GEHGdseva+ws+a++ g+p+ e++ ++ + ++ + + +vr+aayeii +KgaT ygig++++rive lcl|MicrobesOnline__882:209544 163 RGVHAHIVGEHGDSEVALWSRANVSGIPVAEMCARRGIAYDAAFReKALGHVRHAAYEIIGRKGATGYGIGMSLCRIVE 241 ***************************************99998879999***************************** PP TIGR01771 237 ailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkeklkksaetl 297 ail+de++vl+vs+ + g+yg dv l++P+v+g++G+ee+l++++ e+E+++l+ sa++l lcl|MicrobesOnline__882:209544 242 AILHDEHSVLTVSCPVAGHYGLGDVSLSLPCVIGSDGIEEVLDAPIAEDEQAALAASARVL 302 **********************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (309 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: 8.52 // [ok]
This GapMind analysis is from Sep 17 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