Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 313 bits (803), Expect = 7e-90 Identities = 182/476 (38%), Positives = 276/476 (57%), Gaps = 9/476 (1%) Query: 23 YIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWAGRLPAE 82 Y++G A S K A+ +PATG+E+A AD + A+ +A A + W + E Sbjct: 14 YVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPA--WRAKTAKE 71 Query: 83 RERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKIAGKT 142 R IL R+ +L+ E+LA L TLEQGK +A +R EV +++ + A ++ G Sbjct: 72 RAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARG-EVAYGASFIEWFAEEGKRVYGDV 130 Query: 143 LDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSETT 202 IP G + + KEP+GVVA I PWNFP + KV PALAAGC+IV+KP+E T Sbjct: 131 ----IPSFAGNK-RIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDT 185 Query: 203 PLTMLRVAELASEAGIPDGVFNVVTGSGAVC-GAALTSHPHVAKISFTGSTATGKGIART 261 PL+ L +AELA AG+P GVFN+VTGS V G LT+ P V K+SFTGST GK + R Sbjct: 186 PLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKILMRQ 245 Query: 262 AADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEAPLFDT 321 +AD + +V+LELGG P IV DAD ++G + + N GQ C ++R+ ++A ++D Sbjct: 246 SADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDA 305 Query: 322 LVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELIRGSNGPAGE 381 + +AVK ++VG GM P+++ +KV + DA A+ A++ G Sbjct: 306 FAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGKRHGLG 365 Query: 382 GYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTASVWTQNLS 441 G + PT++ ++R+ REE+FGPV L + +A+++ANDTE+GL A +++++ Sbjct: 366 GTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDIG 425 Query: 442 QALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDGWCETKSVCV 497 + +++L+ G V +N L PFGG+KQSG GR+ ++ + E K +CV Sbjct: 426 RVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCV 481 Lambda K H 0.318 0.133 0.402 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: 597 Number of extensions: 32 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: 499 Length of database: 485 Length adjustment: 34 Effective length of query: 465 Effective length of database: 451 Effective search space: 209715 Effective search space used: 209715 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