Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Pf6N2E2_1309 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1309 Length = 486 Score = 336 bits (861), Expect = 1e-96 Identities = 188/480 (39%), Positives = 281/480 (58%), Gaps = 21/480 (4%) Query: 14 FIDGAWVDADNGQTIKVN-NPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKER 72 +IDG V++ + + VN NPATGE +G V GA E +A+ AA +A P W AKER Sbjct: 5 WIDGREVESKD---VFVNYNPATGEAIGEVASGGAEEVAQAVAAAKEAFPKWANTPAKER 61 Query: 73 ATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASF-IEWFAEEAKRIYGDVI 131 A +R+ ELI +N LA L TL+ G P+ + K ++ AS ++FAE R+ G Sbjct: 62 ARLMRKLGELIEQNVPQLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHTY 121 Query: 132 PGHQPDKRLI--VIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSA 189 P D +++ + QP+GV A ++PWN P T K P LA G T VLK + +P +A Sbjct: 122 P---VDDQMLNYTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTA 178 Query: 190 FALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDI 249 L LA AGIP GV +V+ G G L +P VR +SFTG T G+++M + Sbjct: 179 NELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG--L 236 Query: 250 KKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKL 309 KK S+ELGG +P ++F+DADL++A++ A+ + + NG+ C +R++IQ+ VY F + Sbjct: 237 KKYSMELGGKSPVLIFEDADLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEF 296 Query: 310 KVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGG--KPME----- 362 +L +G+ + T G +I + KV +I L +GAT+LAGG +P Sbjct: 297 AARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAHL 356 Query: 363 --GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420 G F +PT+ +V N +A+EE FGP+ L FKDEA+ + ++NDTE+GLASY + +D Sbjct: 357 SRGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALHLANDTEYGLASYIWTQD 416 Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480 +G+ R+A +E GMV +N+ + + PFGG+K SG GREG +Y E + EIK +C+ + Sbjct: 417 IGKAHRLAHGIEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 476 Lambda K H 0.317 0.135 0.390 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: 594 Number of extensions: 26 Number of successful extensions: 4 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: 480 Length of database: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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