Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__HerbieS:HSERO_RS19755 Length = 484 Score = 353 bits (905), Expect = e-101 Identities = 196/477 (41%), Positives = 286/477 (59%), Gaps = 8/477 (1%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI GE T A++ + V+P+ + A A+G + D+ RA++AA+ E G WS S + Sbjct: 8 FIAGEATEASDGQRMNLVNPINEEIYASAAQGTAADVARAVAAAKAQLEGGAWSKLSGLQ 67 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L+KLA L+E + LA ++ G+ D+P A +R A +++ G Sbjct: 68 RGQLLHKLAALVERDTDLLADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQMEGRT 127 Query: 143 ATTSSH----ELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198 T+ + L+ VREP+GV+ AI+PWN PL++T WK+ LAAG +V++KP+E++P Sbjct: 128 IPTAGYMGKPTLSYTVREPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEETPQ 187 Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258 SA+ LA LA+EAG PDGV+NVVTG+G+ G+AL H D+ I+FTGS G+ + + AG+ Sbjct: 188 SALHLARLAQEAGFPDGVINVVTGYGNSVGRALCEHPDVAKISFTGSPEAGRAIQRIAGE 247 Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 KRV LE GGKS IVF D P + A G+F NQGQVC AG+R+L++ S+A F Sbjct: 248 -QFKRVTLELGGKSPQIVFDDAP-FEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQRF 305 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG--RNAGLA 376 L + A G P P MG + A + V+ +I++G +G LL G Sbjct: 306 AKALAEAAAGITVGDPSQPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGGVSRPDKG 365 Query: 377 AAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSR 436 + PTIF D + S++REEIFGPV + F +EE+A+ LANDS+YGL A VWT +L+R Sbjct: 366 WFVQPTIFADANNGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTTNLAR 425 Query: 437 AHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 AHR++ +K G+V VN ++ D +P+GG K SG GR+ L +TE KT+ + L Sbjct: 426 AHRVAAGVKVGAVGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTVTVLL 482 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: 545 Number of extensions: 18 Number of successful extensions: 5 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: 484 Length adjustment: 34 Effective length of query: 461 Effective length of database: 450 Effective search space: 207450 Effective search space used: 207450 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