Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 301 bits (772), Expect = 2e-86 Identities = 169/459 (36%), Positives = 260/459 (56%), Gaps = 4/459 (0%) Query: 16 GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75 G+ V NPATG+ L ++A+ AE+ A+ AADAA W T K RA L + ++I Sbjct: 25 GKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPAWRAKTAKERAAILRRWFELIM 84 Query: 76 ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIR 135 + A L + GKPL A E+ +FA + + G + ++ Sbjct: 85 AAQEDLAVLMTLEQGKPLAEA-RGEVAYGASFIEWFAEEGKRVYGDVIPSFAGNKRIVVL 143 Query: 136 RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPA 194 ++P+GVVA+I PWN+P M K+ PALAAG +V+KP+E TPL+AL LAELA+ PA Sbjct: 144 KEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDTPLSALALAELAERAGVPA 203 Query: 195 GVINILFGRGKT-VGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPV 253 GV NI+ G +G LT P VR +S TGS G+ ++ +A ++K+ +ELGG AP Sbjct: 204 GVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKILMRQSADTVKKVSLELGGNAPF 263 Query: 254 IVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPD 313 IVFDDAD++ V+G Y N+GQ C A R+ Q G+YD KL AV ++ G Sbjct: 264 IVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDAFAAKLAEAVKQIRVGNGM 323 Query: 314 DESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDA 373 + GP+ + +E+V + + +A A G KV GG++ G ++ PT+L G + Sbjct: 324 EAGVTQGPMINGQAVEKVEELMGDALAKG-AKVALGGKRHGLGGTFFEPTILTGVTTEMR 382 Query: 374 IVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN 433 + ++E+FGPV + F+ E + AND+++GLA+ +++D+GR RV+ +L+YG +N Sbjct: 383 VAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDIGRVWRVAEQLEYGMVGIN 442 Query: 434 THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 + P GG K SG G++ S YG+ED+ ++++ V Sbjct: 443 EGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCV 481 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: 529 Number of extensions: 17 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