Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PfGW456L13_1397 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1397 Length = 496 Score = 548 bits (1411), Expect = e-160 Identities = 259/489 (52%), Positives = 355/489 (72%) Query: 9 WEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARA 68 W+++A L+ +A I+G+ A SG+TF ++P + LA VA+C D N AV NAR Sbjct: 7 WQRKAASLRFPDQAVIDGQRRPAQSGQTFAAINPATSQCLANVAACGEEDVNAAVHNARQ 66 Query: 69 TFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAI 128 F +G W+ +P +RK L+R ADL+ +N EELALL++L+MGKP+ D+ +ID+PGAA Sbjct: 67 VFEAGTWAARSPTERKQVLLRLADLILENREELALLDSLNMGKPVADAYNIDVPGAAGVF 126 Query: 129 HWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSV 188 W AE++DK+YD+VAP+ + L +TRE +GVV A+VPWNFPL MA WKL PALA GNSV Sbjct: 127 RWYAESLDKLYDQVAPSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSV 186 Query: 189 VLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKI 248 +LKP+E+SP +A+R+A+LA+EAG+PAGVLNVLPG G GKAL LH DVD LVFTGST++ Sbjct: 187 ILKPAEQSPFSALRLAELALEAGVPAGVLNVLPGLGEQTGKALGLHPDVDCLVFTGSTEV 246 Query: 249 AKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRL 308 K M Y+ +SN+K++WLE GGKS N+VFAD DL AAE AA I FNQGEVC+A SRL Sbjct: 247 GKYFMQYSAQSNLKQVWLECGGKSANLVFADCQDLDLAAEKAAFGIFFNQGEVCSANSRL 306 Query: 309 LVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLL 368 LV+RSI D+F+ + + W PG+PLDP + GA+VD++Q ++ +I+ + GA + Sbjct: 307 LVQRSIHDEFVERLKAQAERWLPGDPLDPSSAAGAIVDSRQTARIMKFIQQAEQQGATRI 366 Query: 369 AGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYG 428 GG++++ +++PTIF GVT M + ++E+FGPVL+V AFD A+ +AND+ YG Sbjct: 367 CGGRQSIINGSDNFIQPTIFTGVTPDMPLFRDEVFGPVLAVTAFDDEAHALQLANDSVYG 426 Query: 429 LAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYT 488 LAA +WT D+++AH+ AR +RAG+V VN D D+T PFGG KQSG GRD SLH+ +KYT Sbjct: 427 LAASLWTDDLNRAHRVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLHSFDKYT 486 Query: 489 ELKATWIKL 497 +LK TW +L Sbjct: 487 QLKTTWFQL 495 Lambda K H 0.316 0.132 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: 644 Number of extensions: 21 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: 497 Length of database: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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: 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