Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PfGW456L13_3141 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3141 Length = 498 Score = 451 bits (1161), Expect = e-131 Identities = 227/493 (46%), Positives = 318/493 (64%), Gaps = 5/493 (1%) Query: 4 LTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAV 63 L+ A++ A+ LK ++F+NGE +VSG TF +P LA++ +C+ D + AV Sbjct: 5 LSAAEYAAIARDLKFPTQSFVNGESYTSVSGNTFTTTNPATNDVLAEITACNAQDVDFAV 64 Query: 64 ENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPG 123 A+ F G W +L+P++RK L+RFADLL +N EL++LE+LD GKP+ + D+P Sbjct: 65 AKAKEAFEDGRWHKLSPSERKKVLLRFADLLEQNSHELSVLESLDSGKPVRECQLTDVPE 124 Query: 124 AAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALA 183 I W AE IDK+YD AP L LV RE +GVVG ++PWNFPLLM WK+GP+LA Sbjct: 125 TIHMIRWHAELIDKIYDSTAPVGPGALSLVVREAIGVVGLVLPWNFPLLMLAWKIGPSLA 184 Query: 184 TGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFT 243 G S+++KP++++ LTA+R+A+LA EAG+PAGV NVL G G VG+ L HMDV + FT Sbjct: 185 AGCSIIVKPAKETTLTALRVAELAHEAGVPAGVFNVLSGGGGEVGEPLGRHMDVSMVSFT 244 Query: 244 GSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCT 303 GST ++ + YA +SN+KRI LE GGK+P +V D DL A + +N GE C+ Sbjct: 245 GSTATGRRFLNYAADSNLKRIVLECGGKNPAVVMNDVEDLDLVASHVVNGAFWNMGENCS 304 Query: 304 AGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKD 363 A SRL+V IKD+ L + ++ WK GNPLDP +GA+V V SY+E + Sbjct: 305 ASSRLIVHADIKDELLKRIGVQMREWKMGNPLDPDNRLGAMVSKAHFEKVRSYLEQAAVE 364 Query: 364 GAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIAN 423 ++ GG + +VEPT+ DGV R+ QEEIFGPVL+V F+T +EA+A+AN Sbjct: 365 KLDVVYGGNTESD----IFVEPTVVDGVGADSRLFQEEIFGPVLAVTTFNTVDEAIALAN 420 Query: 424 DTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSG-NGRDKSLH 482 D+ YGLAA ++T ++ A K +R +RAG V VN + GD + PFGG+K+SG GRDKS+ Sbjct: 421 DSVYGLAASVYTDNLRNAIKLSREIRAGIVTVNCFGEGDASTPFGGYKESGFGGRDKSIW 480 Query: 483 ALEKYTELKATWI 495 A ++YTE+K WI Sbjct: 481 AHDQYTEIKTIWI 493 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: 664 Number of extensions: 31 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: 498 Length adjustment: 34 Effective length of query: 463 Effective length of database: 464 Effective search space: 214832 Effective search space used: 214832 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