Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_040474614.1 MDG893_RS13420 FAD-binding protein
Query= metacyc::MONOMER-15202 (579 letters) >NCBI__GCF_000170835.1:WP_040474614.1 Length = 558 Score = 900 bits (2326), Expect = 0.0 Identities = 432/548 (78%), Positives = 481/548 (87%), Gaps = 1/548 (0%) Query: 33 THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTD 92 T FDYIVVGAGTAGCLLANRLSA+P NRVLLIEAGG+D YHWIHIPVGYLYCI+NPRTD Sbjct: 11 TPEFDYIVVGAGTAGCLLANRLSANPDNRVLLIEAGGKDTYHWIHIPVGYLYCIDNPRTD 70 Query: 93 WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152 WRFRT+P PGLNGRSLIYPRGKTLGGCSSINGMLY+RGQARDY+ WA++TGDDAW W+NC Sbjct: 71 WRFRTDPVPGLNGRSLIYPRGKTLGGCSSINGMLYIRGQARDYNHWADVTGDDAWNWENC 130 Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212 LP FMRHEDHYRLDEGG+AD DH KFHGHGGEWRIE QRLKWQVL DFA AAV+AGVPRT Sbjct: 131 LPYFMRHEDHYRLDEGGNADADHNKFHGHGGEWRIEHQRLKWQVLEDFAEAAVQAGVPRT 190 Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272 DFNRGDNEGVD FEVNQRSGWRWN SKAFLR RGNLT+WHS QVL L+ +G + Sbjct: 191 YDFNRGDNEGVDYFEVNQRSGWRWNTSKAFLRSATNRGNLTLWHSAQVLALNMEPTDGGQ 250 Query: 273 PRCCGVTVERA-GKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLP 331 P C GV V +A G + + A EV+LSAG+IGSPQLLQLSGIGP LL + +IPVVADLP Sbjct: 251 PHCTGVRVAKANGNETLALAAKEVILSAGSIGSPQLLQLSGIGPADLLEQLSIPVVADLP 310 Query: 332 GVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFT 391 GVGENLQDHLQIRS+YK+ GAKTLNTM +SL GKA+IGLEY+ KRSGPMSMAPSQLC FT Sbjct: 311 GVGENLQDHLQIRSVYKLHGAKTLNTMIHSLFGKAQIGLEYLAKRSGPMSMAPSQLCAFT 370 Query: 392 RSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPA 451 RSS +Y++ N++YHVQPLSL+AFGQPLH FPAITASVCNLNP+SRGTVRI S + R AP+ Sbjct: 371 RSSDDYDYANIQYHVQPLSLDAFGQPLHTFPAITASVCNLNPSSRGTVRIHSRDARHAPS 430 Query: 452 ISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGT 511 I+PNYL+T EDR+VAADSLRVTR IA Q AF+KY PEE+KPGV+YQ+D++LARLAGDIGT Sbjct: 431 IAPNYLNTAEDRKVAADSLRVTRRIAQQEAFSKYQPEEYKPGVEYQTDDELARLAGDIGT 490 Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571 TIFHPVGT +MGR +D MAVVDSHL+VRGV GLRVVDA IMPTITSGNTNSPTLMIAEKA Sbjct: 491 TIFHPVGTTRMGRANDEMAVVDSHLQVRGVLGLRVVDAGIMPTITSGNTNSPTLMIAEKA 550 Query: 572 AGWILKSQ 579 A WIL + Sbjct: 551 ANWILNDE 558 Lambda K H 0.318 0.135 0.418 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: 1098 Number of extensions: 35 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: 579 Length of database: 558 Length adjustment: 36 Effective length of query: 543 Effective length of database: 522 Effective search space: 283446 Effective search space used: 283446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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