Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 6936720 Sama_0907 threonine synthase (RefSeq)
Query= BRENDA::P00934 (428 letters) >FitnessBrowser__SB2B:6936720 Length = 428 Score = 487 bits (1254), Expect = e-142 Identities = 252/421 (59%), Positives = 313/421 (74%), Gaps = 2/421 (0%) Query: 1 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60 M+LYNLK +E+VSF+QAV GLGK++GLFFP +P+ L +++ +L L F RS KIL Sbjct: 1 MELYNLKHPDERVSFSQAVKLGLGKDRGLFFPTHIPK--LDDVETLLTLPFAQRSKKILG 58 Query: 61 AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120 A++ DE+ Q +++ V AF F P+ V+ CLELFHGPTLAFKDFG RFMAQ L Sbjct: 59 AWLADELGQNVVDALVDKAFTFEVPLVKVDDTRYCLELFHGPTLAFKDFGARFMAQCLNV 118 Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180 +AGD+ +TILTATSGDTGAAVA AFYGL V+V +LYP+GKIS LQEK+F TLG NI TV Sbjct: 119 LAGDERLTILTATSGDTGAAVADAFYGLDKVQVCVLYPKGKISLLQEKMFTTLGNNIHTV 178 Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240 A++ DFDACQALVKQAFDD +++ L LNSANSINISRLLAQICYYFEAVAQ + + Sbjct: 179 AVESDFDACQALVKQAFDDADVREGLHLNSANSINISRLLAQICYYFEAVAQYRKNFVDA 238 Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300 V++VPSGNFG+LTAG AK++GLPVKRF+AATN NDTVPR+L W T AT+SNA Sbjct: 239 PVIAVPSGNFGNLTAGFFAKAMGLPVKRFVAATNSNDTVPRYLASANWQVNPTVATMSNA 298 Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360 MDV+ P+NWPRVE + + W L E+ A+D++ T+ + L+E GY SEPHAA+A +A Sbjct: 299 MDVADPSNWPRVEAIAKVMGWSLAEIDGVALDEQQTRCALLALQEDGYLSEPHAAIAAQA 358 Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420 L+ L E G+FLGTAHPAKFK+ V+ L L LP ELA AD P+LS NL DFAAL Sbjct: 359 LKATLGKDERGIFLGTAHPAKFKDVVDHELSLDLPLPPELAAVADKPVLSANLAPDFAAL 418 Query: 421 R 421 + Sbjct: 419 K 419 Lambda K H 0.319 0.135 0.395 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: 524 Number of extensions: 15 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: 428 Length of database: 428 Length adjustment: 32 Effective length of query: 396 Effective length of database: 396 Effective search space: 156816 Effective search space used: 156816 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: 51 (24.3 bits)
Align candidate 6936720 Sama_0907 (threonine synthase (RefSeq))
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))
# 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.aa/TIGR00260.hmm # target sequence database: /tmp/gapView.11842.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00260 [M=340] Accession: TIGR00260 Description: thrC: threonine synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-104 333.8 0.1 7.5e-104 333.5 0.1 1.0 1 lcl|FitnessBrowser__SB2B:6936720 Sama_0907 threonine synthase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936720 Sama_0907 threonine synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.5 0.1 7.5e-104 7.5e-104 16 329 .. 68 385 .. 51 391 .. 0.93 Alignments for each domain: == domain 1 score: 333.5 bits; conditional E-value: 7.5e-104 TIGR00260 16 vdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgnetvlcAtsGdtgaaaaeal 92 +++ + ++f+++ + +v y++elfhgPtlaFKD+g +f+a+ l+ ++++ + t+l+AtsGdtgaa+a a+ lcl|FitnessBrowser__SB2B:6936720 68 NVVDALVDKAFTFEVPLVKVDD-TRYCLELFHGPTLAFKDFGARFMAQCLNVLAGDERLTILTATSGDTGAAVADAF 143 5556667778888888888888.77**************************************************** PP TIGR00260 93 agkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaq 166 +g v+v+vLyPkgkis+++ek++t+l +n++++a++ dFD++q+lvk++f+d l lns+Nsin++r++aq lcl|FitnessBrowser__SB2B:6936720 144 YGLDKVQVCVLYPKGKISLLQEKMFTTLGNNIHTVAVESDFDACQALVKQAFDDADvreGLHLNSANSINISRLLAQ 220 ******************99*********************************5444569***************** PP TIGR00260 167 ktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTl 243 ++y+fe+v+q+ k+ d v++vpsgnfg++++Gf++k ++ lp k+++aa++++d+v+r+l s +++ +++T+ lcl|FitnessBrowser__SB2B:6936720 221 ICYYFEAVAQYRKNFVDAPVIAVPSGNFGNLTAGFFAKAMG-LP-VKRFVAATNSNDTVPRYLASANWQVNPTVATM 295 ****************************************9.**.88899988889********************* PP TIGR00260 244 stAmdignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekg.vs... 316 s+Amd+ psn++r++++a+ ++ l +++ + de+ ++ ++++e gyl eph+a+a +alk ++ k+ + lcl|FitnessBrowser__SB2B:6936720 296 SNAMDVADPSNWPRVEAIAKVMGWSLAEIDGVALDEQQTRCALLALQEDGYLSEPHAAIAAQALKATLGKDeRGifl 372 *****************************999***************************************733678 PP TIGR00260 317 atadpaKFeevve 329 +ta+paKF++vv lcl|FitnessBrowser__SB2B:6936720 373 GTAHPAKFKDVVD 385 ***********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (428 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: 8.89 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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