Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PP_2589 PP_2589 Aldehyde dehydrogenase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >FitnessBrowser__Putida:PP_2589 Length = 497 Score = 554 bits (1427), Expect = e-162 Identities = 267/489 (54%), Positives = 352/489 (71%) Query: 9 WEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARA 68 W+QRA DL + A I+G+ +A G TF ++P +L ++A+C A+ AV +AR Sbjct: 7 WQQRASDLYLPAHALIDGKPVNAQDGATFAAINPATNNVLAQVAACGHAEVDLAVASARR 66 Query: 69 TFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQAL 128 F G W R+AP +RK ++R A L+ H EELALL++L+MGKP+ D+ NIDVPG+A Sbjct: 67 AFEQGPWPRMAPGERKKVLLRLAELIMAHREELALLDSLNMGKPVMDAYNIDVPGSAHVF 126 Query: 129 SWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSV 188 +W GEA+DKLYD+VA T + L +TRE +GVV A+VPWNFPL MA WKL PAL+ GNSV Sbjct: 127 AWYGEALDKLYDQVAPTAANALATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSV 186 Query: 189 VLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKI 248 VLKP+E+SP +ALR+A LA+EAG+P+GVLNV+PG G G+AL LH DVD LVFTGST++ Sbjct: 187 VLKPAEQSPFSALRLAQLALEAGVPEGVLNVVPGLGEQAGQALGLHPDVDCLVFTGSTQV 246 Query: 249 AKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRL 308 K M YS +SN+K++WLE GGKSPN+VF + DL AAE AA I FNQGEVC+A SRL Sbjct: 247 GKYFMQYSAQSNLKQVWLECGGKSPNLVFDNCQDLDLAAEKAAFGIFFNQGEVCSANSRL 306 Query: 309 LVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLV 368 V+R+I D F+ + + W PGNPLDPA+ GA+VD Q + + I +GA+LV Sbjct: 307 YVQRAIHDEFIERLQAKARQWLPGNPLDPASRAGAIVDAGQTGRIEAAIVRAGQEGARLV 366 Query: 369 AGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYG 428 GG+R+ E Y+EPTIF GV M +A+EE+FGPVL+V AFDT E+A+ +AND+ YG Sbjct: 367 CGGRRLTIEGSDNYIEPTIFAGVEGRMSLAREEVFGPVLAVSAFDTEEEAVRLANDSIYG 426 Query: 429 LAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYT 488 LAA+VW+ D ++ H A+AL+AG+V VN D D+T PFGG KQSG GRD SLH+FDKY+ Sbjct: 427 LAASVWSDDFNQVHRVARALKAGTVSVNTVDALDVTVPFGGGKQSGFGRDLSLHSFDKYS 486 Query: 489 ELKSTWIKL 497 +LK+TW +L Sbjct: 487 QLKTTWYQL 495 Lambda K H 0.316 0.132 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: 711 Number of extensions: 30 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: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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