Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase
Query= CharProtDB::CH_007936 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS19755 Length = 484 Score = 395 bits (1016), Expect = e-114 Identities = 214/472 (45%), Positives = 294/472 (62%), Gaps = 7/472 (1%) Query: 22 FINNEFVKGVEGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFEG-PWRQVTPSE 80 FI E + +G+ ++NP NE++ S + T DV AVAAA+A EG W +++ + Sbjct: 8 FIAGEATEASDGQRMNLVNPINEEIYASAAQGTAADVARAVAAAKAQLEGGAWSKLSGLQ 67 Query: 81 RGILINKLADLMERDIDTLAAIESLDNGKA-FTMAKVDLANSIGCLRYYAGWADKIHGQT 139 RG L++KLA L+ERD D LA +++ G++ +D+ N+I LR AGWA+++ G+T Sbjct: 68 RGQLLHKLAALVERDTDLLADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQMEGRT 127 Query: 140 IDT----NPETLTYTRHEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPL 195 I T TL+YT EP+GV G I+PWN PL++ SWK+ +AAG TVV+K AE+TP Sbjct: 128 IPTAGYMGKPTLSYTVREPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEETPQ 187 Query: 196 SALYAAKLIKEAGFPAGVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAK 255 SAL+ A+L +EAGFP GVINV++G+G + G A+ H D+ K++FTGS GR I Q A Sbjct: 188 SALHLARLAQEAGFPDGVINVVTGYGNSVGRALCEHPDVAKISFTGSPEAGRAI-QRIAG 246 Query: 256 SNLKKVTLELGGKSPNIVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFV 315 K+VTLELGGKSP IVFDDA ++A+ G+F N GQ C AGSRILVQ + +F Sbjct: 247 EQFKRVTLELGGKSPQIVFDDAPFEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQRFA 306 Query: 316 ARFKERAQKNKVGNPFEQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGNEGY 375 E A VG+P + GP + QF+R+ YI G GAT+ GG ++G+ Sbjct: 307 KALAEAAAGITVGDPSQPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGGVSRPDKGW 366 Query: 376 FIQPTVFTDVTSDMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTA 435 F+QPT+F D + M IA+EEIFGPV TI F E EAI + N + YGLAA V T N+ A Sbjct: 367 FVQPTIFADANNGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTTNLARA 426 Query: 436 IRVSNALKAGTVWINNYNMISYQAPFGGFKQSGLGRELGSYALENYTQIKTV 487 RV+ +K G V +N ++ + P+GG K SG+GRE G YT+ KTV Sbjct: 427 HRVAAGVKVGAVGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTV 478 Lambda K H 0.318 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: 554 Number of extensions: 23 Number of successful extensions: 5 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: 484 Length adjustment: 34 Effective length of query: 463 Effective length of database: 450 Effective search space: 208350 Effective search space used: 208350 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