Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::C6KEM4 (506 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 311 bits (796), Expect = 7e-89 Identities = 191/479 (39%), Positives = 273/479 (56%), Gaps = 38/479 (7%) Query: 9 RRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAAR---DAFSRDGG 65 R G+FIGG ++ P G+ NPA + + GT D+E AV AAR A++R GG Sbjct: 32 RFGVFIGGTFQAP--GKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGG 89 Query: 66 RQWSRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAAC--FEYY 123 + W+R L AIA ++ A+LETLD+GKP+ E S D+D A F Y+ Sbjct: 90 QGWARV--------LYAIARLLQKHSRLFAVLETLDNGKPIRE-SRDIDIPLAQRHFYYH 140 Query: 124 ADLAEALDGKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCT 183 A +A ++ + + P+GV G I PWN+PLLM WK+APALA G T Sbjct: 141 AGMAALMEDELPDRV--------------PVGVCGQIVPWNFPLLMLAWKIAPALAMGNT 186 Query: 184 TILKPSELASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTE 243 +LKP+E ++ L IC E G+PPGV+NI+TG G GA L SH VDK+AFTGST+ Sbjct: 187 VVLKPAEWTPLTALLFAEICGEAGVPPGVVNIVTGDG-ATGAALVSHPGVDKIAFTGSTD 245 Query: 244 TGKRIMTSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRL 303 G+ I + A K ++LELGGKSP +VF+D D+D AVE + I+ N GQVC A SRL Sbjct: 246 VGREIRRATAGTGKALTLELGGKSPYVVFED-ADLDSAVEGLVDAIWFNQGQVCCAGSRL 304 Query: 304 LLHEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATIL 363 L+ E IA+ F +L A +++ DPL++ +G+++ K+ + ++ + E + Sbjct: 305 LVQEGIAEAFYAKLRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNGE---VH 361 Query: 364 YGGGRPQHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423 G P G F PT+IT + + + ++E+FGPV+ FRT +EAVE+AN T YG Sbjct: 362 QPGTVP---AEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYG 418 Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNY 482 LA + S + R I+ L +G++W+N + A +GG + SGFGRE G GL Y Sbjct: 419 LAATLWSENINRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAY 477 Score = 92.8 bits (229), Expect = 4e-23 Identities = 79/281 (28%), Positives = 119/281 (42%), Gaps = 15/281 (5%) Query: 12 LFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRA 71 ++IGG P G PV +P +G P G+ +D+ AV AA A S W R Sbjct: 510 MYIGGKQARPDSGYSRPVWSPKG-VLLGHAPEGSRKDIRNAVEAATGAAS------WGRT 562 Query: 72 PGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYADLAEALD 131 G +RA L +A + R E A +G + A ++ YA A+ D Sbjct: 563 TGHLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYD 622 Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191 G + +P+ + + EP+GV+G P + PLL A + ALA G +L PSE Sbjct: 623 GAVKP---VPIRGV-ALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEP 678 Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251 ++ +L + +P GV+NI+TG PL+SH VD V + I Sbjct: 679 FPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIEAE 738 Query: 252 AAQMVKPVSLELGGKSPLIVFDDIGDIDKAVE----WTMFG 288 AA +K + G + D + +A E W +G Sbjct: 739 AAGNLKRTWVNHGRARDWMQVDARSFLAQATETKTIWVPYG 779 Lambda K H 0.318 0.136 0.418 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: 1050 Number of extensions: 40 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 506 Length of database: 780 Length adjustment: 38 Effective length of query: 468 Effective length of database: 742 Effective search space: 347256 Effective search space used: 347256 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: 54 (25.4 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