Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 306 bits (784), Expect = 2e-87 Identities = 184/464 (39%), Positives = 264/464 (56%), Gaps = 19/464 (4%) Query: 22 LFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81 +FI G T A +TF T +P LA++ +G DI+ A++AAR + W+ Sbjct: 35 VFIGG--TFQAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRA--QPAWARLGGQ 90 Query: 82 KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141 VL +A L++ H+ A+LETLD GKPIR S DIP A R ++A + E Sbjct: 91 GWARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDE 150 Query: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201 + R PVGV IVPWNFPLL+ WK+ PALA GN+V+LKP+E +PL+A+ Sbjct: 151 LPD----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTAL 200 Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261 A + EAG+P GV+N+VTG G G AL H +D IAFTGST G+++ + + Sbjct: 201 LFAEICGEAGVPPGVVNIVTGDG-ATGAALVSHPGVDKIAFTGSTDVGREIRRATAGTG- 258 Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321 K + LE GGKS +VF D DL A I++NQGQVC AG+RLL++E IA+ F A Sbjct: 259 KALTLELGGKSPYVVFEDA-DLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAK 317 Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIGP 381 L+ + + G PLD +G ++D AH V + S G++ G A P Sbjct: 318 LRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMV--AGSNGEVHQPGTVPAEGAFYPP 375 Query: 382 TIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMS 441 T+ ++P L R+EIFGPVLV T F + +A+++AN ++YGL A +W+ +++RA ++ Sbjct: 376 TLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDIA 435 Query: 442 RRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTE 485 +L AG V+VN N D FGG ++SG GR+ L +T+ Sbjct: 436 PKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTK 479 Score = 95.9 bits (237), Expect = 5e-24 Identities = 72/223 (32%), Positives = 107/223 (47%), Gaps = 7/223 (3%) Query: 48 LAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETL 107 L G DI A+ AA G W ++ R +L +A+ + A EE A Sbjct: 535 LGHAPEGSRKDIRNAVEAATGA---ASWGRTTGHLRAQILYYVAENLSARTEEFATRIAE 591 Query: 108 DTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPW 167 TG + + ++ A + YA DK G V +A+ + EPVGVI A P Sbjct: 592 MTGSRVPRA-EAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVIGAFAPD 650 Query: 168 NFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEA 227 + PLL LG ALA GN ++L PSE PL+A L + + +P GV+N+VTG Sbjct: 651 DAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGAHEAL 710 Query: 228 GQALSRHNDIDAI-AFTGSTRTGKQLLKDAGDSNMKRVWLEAG 269 + L+ H +DA+ +F+G+ + + AG N+KR W+ G Sbjct: 711 AKPLASHLGVDAVWSFSGADISTTIEAEAAG--NLKRTWVNHG 751 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: 941 Number of extensions: 58 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 495 Length of database: 780 Length adjustment: 37 Effective length of query: 458 Effective length of database: 743 Effective search space: 340294 Effective search space used: 340294 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: 53 (25.0 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