Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_068465058.1 APY04_RS16355 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_001541235.1:WP_068465058.1 Length = 384 Score = 429 bits (1103), Expect = e-125 Identities = 208/376 (55%), Positives = 262/376 (69%), Gaps = 7/376 (1%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 KPT P NP FSSGPC+K PG+S++ L GRSHRS GK++L I +T +L LP Sbjct: 6 KPTLRPANPHFSSGPCSKRPGWSLDALSGALVGRSHRSPVGKQRLKLVIDKTHALLQLPH 65 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 DY V IVP SDTGAFEM LW++LG RGVDVL WE F W DI +L++ D RV A+Y Sbjct: 66 DYRVAIVPGSDTGAFEMALWNLLGARGVDVLAWEDFGHRWVRDIIAELRIADARVLAADY 125 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G LPDL VDF DV+ WNGT +GV+VP+ WI DR+G+ + DATSA+FA I + K+ Sbjct: 126 GHLPDLAAVDFDRDVILPWNGTAAGVRVPDGAWIAADRKGLIIVDATSALFAQRIDWAKV 185 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241 DV TFSWQK+LGGE AHGM++LSPRA++RL+++ P+WP+PK+FRLT+GGKL DIFAG T Sbjct: 186 DVATFSWQKILGGEAAHGMIVLSPRAIERLQNHRPSWPVPKLFRLTEGGKLQHDIFAGVT 245 Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPSML ED+L TL WA+SVGGL L R + AV ++A+ WI LA RS Sbjct: 246 INTPSMLCVEDYLDTLAWADSVGGLDALCARADATAAVLFDWIARTPWIANLAVDPATRS 305 Query: 302 STSVCFKVDLSDEK-------LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKED 354 +TSVC + + E ++ LE E VAYDIG+YR AP+GLR+WCGATVE+ D Sbjct: 306 NTSVCMRFTDAGEGPGAEQRITDGIVSLLESEGVAYDIGAYRGAPAGLRVWCGATVERSD 365 Query: 355 LECLCEWIEWAYNLVK 370 +E L W+EWAY V+ Sbjct: 366 VEALIPWLEWAYAQVR 381 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: 490 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: 370 Length of database: 384 Length adjustment: 30 Effective length of query: 340 Effective length of database: 354 Effective search space: 120360 Effective search space used: 120360 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_068465058.1 APY04_RS16355 (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.461114.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-181 587.1 0.5 9e-181 586.9 0.5 1.0 1 NCBI__GCF_001541235.1:WP_068465058.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001541235.1:WP_068465058.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 586.9 0.5 9e-181 9e-181 1 373 [. 10 379 .. 10 380 .. 0.98 Alignments for each domain: == domain 1 score: 586.9 bits; conditional E-value: 9e-181 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 rpanp+fssgpc+krpg+s+++l a +grshrs +gk++lk i+kt +l++p dy++ iv++sdtga+em NCBI__GCF_001541235.1:WP_068465058.1 10 RPANPHFSSGPCSKRPGWSLDALSGALVGRSHRSPVGKQRLKLVIDKTHALLQLPHDYRVAIVPGSDTGAFEM 82 7************************************************************************ PP TIGR01365 74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146 alw llgargvd+la+e fg+ wv d++ +l++ d rvl a+yg+lpdl+ vdf++dv++ wngt++gvrvp+ NCBI__GCF_001541235.1:WP_068465058.1 83 ALWNLLGARGVDVLAWEDFGHRWVRDIIAELRIADARVLAADYGHLPDLAAVDFDRDVILPWNGTAAGVRVPD 155 ************************************************************************* PP TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219 g +i+adr+gl i datsa faq++d+ k+dv tfswqk+lgge ahg+++lspra++rl+ ++p+wp+pk+f NCBI__GCF_001541235.1:WP_068465058.1 156 GAWIAADRKGLIIVDATSALFAQRIDWAKVDVATFSWQKILGGEAAHGMIVLSPRAIERLQNHRPSWPVPKLF 228 ************************************************************************* PP TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292 rlt+ggkl++dif g tintpsml+ved+ld+l wa+s+ggl+al arad+ +avl +++a+++w+ la+ + NCBI__GCF_001541235.1:WP_068465058.1 229 RLTEGGKLQHDIFAGVTINTPSMLCVEDYLDTLAWADSVGGLDALCARADATAAVLFDWIARTPWIANLAVDP 301 ************************************************************************* PP TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365 ++rsntsvc++++d e+ ++ ++vs+le egvaydig+yr apaglr+wcgatve+sd+eal++ NCBI__GCF_001541235.1:WP_068465058.1 302 ATRSNTSVCMRFTDAGEGPGAEQ---RITDGIVSLLESEGVAYDIGAYRGAPAGLRVWCGATVERSDVEALIP 371 ************99776555554...7899******************************************* PP TIGR01365 366 wldwafal 373 wl+wa+a NCBI__GCF_001541235.1:WP_068465058.1 372 WLEWAYAQ 379 ******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (384 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: 28.39 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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