Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_011318017.1 AVA_RS05940 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_000204075.1:WP_011318017.1 Length = 392 Score = 467 bits (1202), Expect = e-136 Identities = 228/378 (60%), Positives = 282/378 (74%), Gaps = 10/378 (2%) Query: 3 PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62 PT P+ FSSGPCAKHPG+SV L++ GRSHRS+ GK KL+E I+R++ +LGLP D Sbjct: 8 PTNKPQVTHFSSGPCAKHPGWSVSNLENACLGRSHRSEDGKAKLSEVIERSKQILGLPAD 67 Query: 63 YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122 Y +GIVPASDTGA EM LWS+LG R +D+L WESF + W D+ +LKL D R+ +A YG Sbjct: 68 YRLGIVPASDTGAVEMALWSLLGQRPLDILAWESFGQEWVKDVVDELKLPDVRLLKAPYG 127 Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182 LP+L +VDF +DVVF+WNGTTSGV+VPN DWI DDR+G+T+CDATSA+FAMDIP+ K+D Sbjct: 128 GLPNLDEVDFSHDVVFLWNGTTSGVRVPNGDWIKDDRQGLTICDATSAVFAMDIPWEKID 187 Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242 V+T+SWQKVLGGE HG+++LSPRAV+RL++Y PAWP+PKIFRL++ GKL + IF G TI Sbjct: 188 VLTYSWQKVLGGEAQHGVIVLSPRAVERLQTYEPAWPIPKIFRLSQKGKLIEGIFKGDTI 247 Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302 NTPSML ED L L WAESVGGL LI R+ NLA +V ++NW FLAE E RS Sbjct: 248 NTPSMLCVEDALDALIWAESVGGLPGLISRSEANLAAIAQWVKQSNWADFLAEKPETRSC 307 Query: 303 TSVCFKV------DLSDEK----LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352 TS+C K+ LS E K+L K LEK++VAYDI YR AP GLRIW GATVE Sbjct: 308 TSICLKIVDAAFASLSAEDQGKFAKKLAKLLEKQQVAYDIAPYRAAPPGLRIWGGATVET 367 Query: 353 EDLECLCEWIEWAYNLVK 370 D+E L W++WAY VK Sbjct: 368 ADIEALLPWLDWAYANVK 385 Lambda K H 0.319 0.136 0.430 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: 501 Number of extensions: 12 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: 370 Length of database: 392 Length adjustment: 30 Effective length of query: 340 Effective length of database: 362 Effective search space: 123080 Effective search space used: 123080 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_011318017.1 AVA_RS05940 (phosphoserine transaminase)
to HMM TIGR01365 (phosphoserine aminotransferase (EC 2.6.1.52))
# 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/TIGR01365.hmm # target sequence database: /tmp/gapView.14341.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01365 [M=374] Accession: TIGR01365 Description: serC_2: phosphoserine aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-193 627.3 0.3 5.6e-193 627.0 0.3 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011318017.1 AVA_RS05940 phosphoserine transa Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011318017.1 AVA_RS05940 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 627.0 0.3 5.6e-193 5.6e-193 2 373 .. 12 383 .. 11 384 .. 0.99 Alignments for each domain: == domain 1 score: 627.0 bits; conditional E-value: 5.6e-193 TIGR01365 2 panpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtga 70 p+ +fssgpcak+pg+sv +l na lgrshrs+ gk+kl e ie+++++l++pady++giv+asdtga lcl|NCBI__GCF_000204075.1:WP_011318017.1 12 PQVTHFSSGPCAKHPGWSVSNLENACLGRSHRSEDGKAKLSEVIERSKQILGLPADYRLGIVPASDTGA 80 77789**************************************************************** PP TIGR01365 71 vemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngtt 139 vemalwsllg+r++d+la+esfg++wv dv+ +lkl+dvr l+a+yg lp+l vdf++dvvf wngtt lcl|NCBI__GCF_000204075.1:WP_011318017.1 81 VEMALWSLLGQRPLDILAWESFGQEWVKDVVDELKLPDVRLLKAPYGGLPNLDEVDFSHDVVFLWNGTT 149 ********************************************************************* PP TIGR01365 140 sgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarles 208 sgvrvpngd+i +dr+glticdatsa+fa+d+++ek+dv+t+swqkvlgge hgv++lsprav+rl++ lcl|NCBI__GCF_000204075.1:WP_011318017.1 150 SGVRVPNGDWIKDDRQGLTICDATSAVFAMDIPWEKIDVLTYSWQKVLGGEAQHGVIVLSPRAVERLQT 218 ********************************************************************* PP TIGR01365 209 ytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavlea 277 y+pawp+pkifrl++ gkl+++if+g+tintpsml+vedaldal waes+ggl l++r+++nla +++ lcl|NCBI__GCF_000204075.1:WP_011318017.1 219 YEPAWPIPKIFRLSQKGKLIEGIFKGDTINTPSMLCVEDALDALIWAESVGGLPGLISRSEANLAAIAQ 287 ********************************************************************* PP TIGR01365 278 fvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapag 346 +v++s+w dfla+++e+rs ts+clk+vd + a l ++ q +fak+l+++lek++vaydi yr ap+g lcl|NCBI__GCF_000204075.1:WP_011318017.1 288 WVKQSNWADFLAEKPETRSCTSICLKIVDAAFASLSAEDQGKFAKKLAKLLEKQQVAYDIAPYRAAPPG 356 ********************************************************************* PP TIGR01365 347 lriwcgatveksdleallewldwafal 373 lriw gatve+ d+eall+wldwa+a lcl|NCBI__GCF_000204075.1:WP_011318017.1 357 LRIWGGATVETADIEALLPWLDWAYAN 383 *************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (392 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: 10.93 // [ok]
This GapMind analysis is from Apr 10 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