Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate RR42_RS21485 RR42_RS21485 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS21485 Length = 454 Score = 437 bits (1125), Expect = e-127 Identities = 215/449 (47%), Positives = 300/449 (66%), Gaps = 5/449 (1%) Query: 48 LAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETL 107 L ++ +CD D + AV A+A F G W + +PA+ KA L+RFADLL ++ ELA++E+L Sbjct: 1 LPEITACDALDVDIAVAKAKAAFEDGRWHRRSPAQCKATLLRFADLLEQHAHELAVMESL 60 Query: 108 DMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPW 167 D GKPI + + D+P I W AE IDK+YD AP + L LV REP+GVVG ++PW Sbjct: 61 DSGKPIRECQATDVPETIHTIRWHAELIDKIYDSTAPVGSNALSLVVREPIGVVGLVLPW 120 Query: 168 NFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTV 227 NFPLLM WK+GP+LA G S+++KP++++ LTA+R+A+LA EAG+PAGV NVLPG G V Sbjct: 121 NFPLLMLAWKIGPSLAAGCSIIVKPAKETTLTALRVAELAHEAGVPAGVFNVLPGGGKDV 180 Query: 228 GKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAA 287 G+ L HMDV + FTGST + + YA +SN+KRI LE GGK+P +V D D+ A Sbjct: 181 GEPLGKHMDVSMVSFTGSTDTGRLFLRYAADSNLKRIVLECGGKNPAVVMNDVEDIDVVA 240 Query: 288 EAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDT 347 + + +N GE C+A SRL+V +KD L + L+ WK G+PLDP+ +G+LV Sbjct: 241 QHVVNGAFWNMGENCSASSRLIVHAEVKDNLLAHIGVHLREWKMGDPLDPEHRIGSLVSE 300 Query: 348 QQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVL 407 SYIE + + ++ GG G T+VEPT+ DGV R+ +EEIFGP+L Sbjct: 301 SHFRKGQSYIELANAENLRVAFGG----GTEGETFVEPTVVDGVGQHSRLFKEEIFGPIL 356 Query: 408 SVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPF 467 SV F + EEA+A+AND+ YGLAA ++TS+++ A + +R +RAG V VN + GD+T PF Sbjct: 357 SVTTFTSTEEAIALANDSVYGLAASVYTSNLNNAIRLSREIRAGVVTVNCFGEGDVTTPF 416 Query: 468 GGFKQSG-NGRDKSLHALEKYTELKATWI 495 GG+K+SG GRDKS+ A ++YTE+K WI Sbjct: 417 GGYKESGFGGRDKSIWAHDQYTEIKTIWI 445 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: 595 Number of extensions: 16 Number of successful extensions: 3 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: 454 Length adjustment: 33 Effective length of query: 464 Effective length of database: 421 Effective search space: 195344 Effective search space used: 195344 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: 51 (24.3 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