Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_012113223.1 XAUT_RS06035 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_000017645.1:WP_012113223.1 Length = 391 Score = 482 bits (1241), Expect = e-141 Identities = 235/378 (62%), Positives = 275/378 (72%), Gaps = 10/378 (2%) Query: 3 PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62 PT P+NP FSSGPCAK PG+++E L D P GRSHR+K GK KL EAI TRD+L +P D Sbjct: 7 PTTRPENPNFSSGPCAKRPGWTLEALSDAPLGRSHRAKVGKAKLKEAIDLTRDVLEVPAD 66 Query: 63 YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122 Y +GIVPASDTGA EM LWSMLG R VD+L WESF +GW TD+ KQLKL D R A YG Sbjct: 67 YKIGIVPASDTGAVEMVLWSMLGARPVDMLAWESFGEGWVTDVVKQLKLTDARALTAPYG 126 Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182 LPDL +VDF +DVVF WNGTTSGV VP+A+WIP DR G+T+CDATSA FA + + KLD Sbjct: 127 ALPDLTQVDFSHDVVFTWNGTTSGVMVPDAEWIPADRTGLTICDATSAAFAQKLDFAKLD 186 Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242 V+TFSWQKVLGGEGAHG+LILSPRAV+RLE+Y PAWPLPKIFR+TKGGKL + IF G TI Sbjct: 187 VVTFSWQKVLGGEGAHGILILSPRAVERLETYKPAWPLPKIFRMTKGGKLIEGIFEGETI 246 Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302 NTPSML ED+L LKWA++VGGL L R+N N +V W+ FLA RS+ Sbjct: 247 NTPSMLCVEDYLDALKWAKNVGGLSALQERSNRNFEAIAQWVHNTPWVDFLATDPVTRSN 306 Query: 303 TSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352 TSVC KV D K + LEK +AYDIG+YRDAP GLRIWCGATVE+ Sbjct: 307 TSVCLKVVDADVTSLPADAQAAFAKAIASGLEKGGIAYDIGAYRDAPPGLRIWCGATVER 366 Query: 353 EDLECLCEWIEWAYNLVK 370 D+E L W++WA+ K Sbjct: 367 ADVEALTHWLDWAFTEAK 384 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: 511 Number of extensions: 17 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: 391 Length adjustment: 30 Effective length of query: 340 Effective length of database: 361 Effective search space: 122740 Effective search space used: 122740 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_012113223.1 XAUT_RS06035 (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.2495791.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-214 696.9 1.1 3.8e-214 696.7 1.1 1.0 1 NCBI__GCF_000017645.1:WP_012113223.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000017645.1:WP_012113223.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 696.7 1.1 3.8e-214 3.8e-214 1 372 [. 10 381 .. 10 383 .. 1.00 Alignments for each domain: == domain 1 score: 696.7 bits; conditional E-value: 3.8e-214 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 rp+np+fssgpcakrpg+++e+l +a+lgrshr+k+gk+klkeai+ tr+vlevpady+igiv+asdtgavem NCBI__GCF_000017645.1:WP_012113223.1 10 RPENPNFSSGPCAKRPGWTLEALSDAPLGRSHRAKVGKAKLKEAIDLTRDVLEVPADYKIGIVPASDTGAVEM 82 79*********************************************************************** PP TIGR01365 74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146 +lws+lgar+vd+la+esfg+gwvtdv+kqlkl d r l a+yg lpdl++vdf++dvvftwngttsgv vp+ NCBI__GCF_000017645.1:WP_012113223.1 83 VLWSMLGARPVDMLAWESFGEGWVTDVVKQLKLTDARALTAPYGALPDLTQVDFSHDVVFTWNGTTSGVMVPD 155 ************************************************************************* PP TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219 +++ipadr glticdatsaafaq+ld+ kldvvtfswqkvlggegahg+lilsprav+rle+y+pawplpkif NCBI__GCF_000017645.1:WP_012113223.1 156 AEWIPADRTGLTICDATSAAFAQKLDFAKLDVVTFSWQKVLGGEGAHGILILSPRAVERLETYKPAWPLPKIF 228 ************************************************************************* PP TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292 r+tkggkl+++ifegetintpsml+ved+ldalkwa+ +ggl+al++r++ n + ++++v +++wvdfla+ + NCBI__GCF_000017645.1:WP_012113223.1 229 RMTKGGKLIEGIFEGETINTPSMLCVEDYLDALKWAKNVGGLSALQERSNRNFEAIAQWVHNTPWVDFLATDP 301 ************************************************************************* PP TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365 +rsntsvclkvvd dv+ l++daqa fak ++s lek g+aydig+yrdap+glriwcgatve+ d+eal++ NCBI__GCF_000017645.1:WP_012113223.1 302 VTRSNTSVCLKVVDADVTSLPADAQAAFAKAIASGLEKGGIAYDIGAYRDAPPGLRIWCGATVERADVEALTH 374 ************************************************************************* PP TIGR01365 366 wldwafa 372 wldwaf+ NCBI__GCF_000017645.1:WP_012113223.1 375 WLDWAFT 381 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (391 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: 00:00:00.00 # Mc/sec: 23.04 // [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