Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate PfGW456L13_3205 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3205 Length = 471 Score = 208 bits (529), Expect = 4e-58 Identities = 160/463 (34%), Positives = 235/463 (50%), Gaps = 25/463 (5%) Query: 2 KSLYIAGEWLAGGGEAF-ESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60 K+L+I G W G E +NP T++ S VE+AV +AR+AF W+R Sbjct: 5 KTLFIDGRWQTPSGRGIAEVINPATEEACGSVPLGDELDVENAVASARRAFASWSRTPSS 64 Query: 61 ERISVLEAFAAALKNHADELAHTIGEETGKPL-WEAATEVTSMVNKIA--ISVQSYRERT 117 R + A A L+N ADE+A I E G P+ W + +V + + + + + Sbjct: 65 VRAGYIRALADQLRNRADEMAAVITTELGMPVQWCRSVQVDGPITGLEQYVELAHLMDEV 124 Query: 118 GEKSGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKV 177 E L AV GV A P+N+P H G + PAL AG +V+ KPS+ TP Sbjct: 125 REVGNSLVIREAV------GVCAFINPWNYPLHQLIGKLAPALAAGCTVVVKPSQETPLH 178 Query: 178 AELTVKCWIEAGLPAGVLNLLQG-ARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGR 236 A L + + GLPAGV NL+ G + G ALA +P +D + FTGS+ G + Q A Sbjct: 179 AFLLAQMIEDIGLPAGVFNLVSGPGSKVGEALAKHPDVDMVSFTGSTGAGVRV-AQAAAP 237 Query: 237 PDKILALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLL 296 K + LE+GG +PL++ + ADL AAV +Q I++GQ CT R+L+P + +++ Sbjct: 238 SVKRVCLELGGKSPLLIAEDADLAAAVRYGVQDVMINSGQTCTALTRMLLPASRYAEAV- 296 Query: 297 ARLVAVSSTLSVGAFDQ-QPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQA- 354 +A++ TLS+ D P F+G + S G + ++D + GA L P Sbjct: 297 --ELALAETLSLRMGDPLDPQSFLGPMCSAGQKRTVLDYIKVGQQEGARLLCGGDTPSTF 354 Query: 355 -QSALLTPGIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDS 412 + ++P + DV EE+FGP+L +I YAD AI AND+ +GL++G+ + S Sbjct: 355 ERGFYVSPTLFADVDNRMRIAQEEIFGPVLCLIPYADETQAIQIANDSPFGLSSGVWAGS 414 Query: 413 EARYQQFWLESRAGIVNWNKQLTGAASS--APFGGVGASGNHR 453 R Q + RAG L GAA + APFGG SGN R Sbjct: 415 AERALQLGRQLRAG----QCFLNGAAFNYQAPFGGYKQSGNGR 453 Lambda K H 0.316 0.132 0.388 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: 527 Number of extensions: 24 Number of successful extensions: 6 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: 488 Length of database: 471 Length adjustment: 34 Effective length of query: 454 Effective length of database: 437 Effective search space: 198398 Effective search space used: 198398 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 (21.6 bits) S2: 51 (24.3 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