Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__HerbieS:HSERO_RS05645 Length = 493 Score = 322 bits (824), Expect = 2e-92 Identities = 190/469 (40%), Positives = 271/469 (57%), Gaps = 16/469 (3%) Query: 13 SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLAD 72 + +G + V +PATG V + + A AAV AA AAFA W T K RA + + D Sbjct: 25 AADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRAGIIKRWND 84 Query: 73 VIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTS 132 ++ + L SR GKPL A E+ +F A NG + G Sbjct: 85 LLLAHQDDLGRLISREQGKPLAEA-KGEVAYAASYVEWFGEEATRANGDIIPAPVTGRRM 143 Query: 133 MIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI- 191 M ++P+GVVA+I PWN+P M A K+APALAAG VV KP+E TPLT+L L LA++ Sbjct: 144 MALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALVRLAQEAG 203 Query: 192 FPAGVINILFG---RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELG 248 P GVINI+ R V D +VR +S TGS A G+H+ H+A ++K+ +ELG Sbjct: 204 VPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLKKLSLELG 263 Query: 249 GKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLK 308 G AP IVFDDAD++A ++GV + N GQ C + RIY Q+ +YD V+KLGA VA LK Sbjct: 264 GNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLGARVAALK 323 Query: 309 SGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY----YYAPTL 364 G D ++++GP+ + + ++ + V +A A G +VITGG++ +G G+ YYAPT+ Sbjct: 324 VGPATDPASQIGPMINARAIAKIDQHVRDAIARG-ARVITGGKRLQGPGFGSDNYYAPTV 382 Query: 365 LA---GALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRV 421 LA GA+Q +E FGPV +T F E++V+ AN + +GLA+ ++ DV R HRV Sbjct: 383 LADVTGAMQCSC---EETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRIHRV 439 Query: 422 SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 + L+ G VN + P GG K SGYG++ S++GL+DY ++V Sbjct: 440 TDALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYLHTKYV 488 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: 555 Number of extensions: 32 Number of successful extensions: 6 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: 493 Length adjustment: 34 Effective length of query: 440 Effective length of database: 459 Effective search space: 201960 Effective search space used: 201960 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