Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 297 bits (761), Expect = 5e-85 Identities = 175/466 (37%), Positives = 262/466 (56%), Gaps = 5/466 (1%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66 I+G GE ++ V NPA+ +V+ ++ +AS + A+ AA A EW + + RA Sbjct: 16 IDGRWTVGE-QRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANERAAL 74 Query: 67 LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126 + K +++ E+ + L + GKPL A EI +FA + + G Sbjct: 75 MRKWFNLMMEHQEDLGRLLTLEQGKPLAEA-KGEIAYGAAFIDWFAEEGKRVYGDTIPAP 133 Query: 127 LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE 186 ++ + P+GVVASI PWN+P M A K A ALAAG V +PS +TPL+AL +AE Sbjct: 134 ANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAMAE 193 Query: 187 LAKDI-FPAGVINILFGRGKT-VGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 LA+ PAGV NI+ G +G LT HP V + TGS A G+ +++ A+S+K+ Sbjct: 194 LAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKKVS 253 Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304 MELGG AP IVFDDADI+A V+G Y NAGQ C RI+ QKG+ EK AAV Sbjct: 254 MELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFTEKFTAAV 313 Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364 A LK G + +GP+ S ++ V K V++ A+G K++TGG+ + + AP + Sbjct: 314 ANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASG-AKLVTGGQPSELGESFLAPVI 372 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 + + + + E+FGPV + FD+E + + AND++YGLA+ + +D+GR RV+ Sbjct: 373 VTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGRIFRVAEG 432 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 L+YG VN + + P GG K SG G++ S YGL+DY ++++ Sbjct: 433 LEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYL 478 Lambda K H 0.317 0.134 0.397 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: 553 Number of extensions: 25 Number of successful extensions: 4 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: 474 Length of database: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 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: 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