Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PfGW456L13_1397 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1397 Length = 496 Score = 511 bits (1317), Expect = e-149 Identities = 258/492 (52%), Positives = 341/492 (69%), Gaps = 4/492 (0%) Query: 6 LAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSA 65 L YWQ KA SL ++ I+G+ A +TF ++P T LA +A D++ A+ Sbjct: 4 LEYWQRKAASLRFPDQAVIDGQRRPAQSGQTFAAINPATSQCLANVAACGEEDVNAAVHN 63 Query: 66 ARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAA 125 AR VFE G W+ SP +RK VL +LADL+ + EELALL++L+ GKP+ + D+PGAA Sbjct: 64 ARQVFEAGTWAARSPTERKQVLLRLADLILENREELALLDSLNMGKPVADAYNIDVPGAA 123 Query: 126 RAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAG 185 RWYAE++DK+Y +VA ++ + LA I RE +GV+AA+VPWNFPL + WKL PALAAG Sbjct: 124 GVFRWYAESLDKLYDQVAPSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAG 183 Query: 186 NSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGS 245 NSVILKP+E+SP SA+RLA LA EAG+P GVLNV+ G G + G+AL H D+D + FTGS Sbjct: 184 NSVILKPAEQSPFSALRLAELALEAGVPAGVLNVLPGLGEQTGKALGLHPDVDCLVFTGS 243 Query: 246 TRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAG 305 T GK ++ + SN+K+VWLE GGKSAN+VFADC DL AA A GIF+NQG+VC A Sbjct: 244 TEVGKYFMQYSAQSNLKQVWLECGGKSANLVFADCQDLDLAAEKAAFGIFFNQGEVCSAN 303 Query: 306 TRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQ 365 +RLL++ SI DEF+ LK QA+ W PG PLDP++ G ++D + FI++ E +G Sbjct: 304 SRLLVQRSIHDEFVERLKAQAERWLPGDPLDPSSAAGAIVDSRQTARIMKFIQQAEQQGA 363 Query: 366 L-LLDGRNA---GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421 + GR + G I PTIF V P+ L R+E+FGPVL VT F E ALQLANDS Sbjct: 364 TRICGGRQSIINGSDNFIQPTIFTGVTPDMPLFRDEVFGPVLAVTAFDDEAHALQLANDS 423 Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481 YGL A++WT DL+RAHR++R+L+AG+V VN+ + D+TVPFGG KQSG GRD SLH+ + Sbjct: 424 VYGLAASLWTDDLNRAHRVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLHSFD 483 Query: 482 KFTELKTIWISL 493 K+T+LKT W L Sbjct: 484 KYTQLKTTWFQL 495 Lambda K H 0.317 0.133 0.389 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: 638 Number of extensions: 20 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: 495 Length of database: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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