Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_041243432.1 GLOV_RS13735 succinate-semialdehyde dehydrogenase I
Query= BRENDA::C6KEM4 (506 letters) >NCBI__GCF_000020385.1:WP_041243432.1 Length = 484 Score = 310 bits (794), Expect = 7e-89 Identities = 176/478 (36%), Positives = 263/478 (55%), Gaps = 11/478 (2%) Query: 9 RRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQW 68 R+ ++ G W G+ + V NPAT +G IP + A+ AA A+ W Sbjct: 11 RQSCYLNGQWLAADSGKTIDVTNPATGEVLGTIPKMGTAETRRAIEAADAAWPA-----W 65 Query: 69 SRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACFEYYADLAE 128 RA LR + + + +LA++ T + GKPL E+ G++ A+ E++A+ + Sbjct: 66 RAKTAKERATILRRWFELMLENQEDLAVIMTAEQGKPLAESRGEISYAASFIEWFAEEGK 125 Query: 129 ALDGKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKP 188 L G I + + V+KEPIGV ITPWN+P M T K PALAAGCT ++KP Sbjct: 126 RLYG---DTIPAHAADKRIVVIKEPIGVCAAITPWNFPSAMITRKAGPALAAGCTMVVKP 182 Query: 189 SELASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRI 248 + S L L + G+P GV ++ITG E G ++S+ + K+ FTGSTE GK++ Sbjct: 183 ATATPFSALALAELGERAGIPAGVFSVITGSSSEIGTEMTSNPIIRKLTFTGSTEIGKQL 242 Query: 249 MTSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVCSATSRLLLHEK 308 A +K VS+ELGG +P IVFDD D+D AVE + + N GQ C T+RLL+ Sbjct: 243 TAQCAATMKKVSMELGGNAPFIVFDD-ADLDAAVEGAIASKYRNTGQTCVCTNRLLVQAG 301 Query: 309 IAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGGGR 368 + F ++L ++V D L++ + G +I E +K+++ I A S+GA I GG R Sbjct: 302 VYDLFAEKLATAVAKMRVGDGLKDDVQQGPLIDEASVQKVEEHIHDAVSKGARIALGGKR 361 Query: 369 PQHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYGLAGAV 428 H G F +PTI+ DV+ M + +EE FGPV + +F TD+EA+ +ANDT +GLA Sbjct: 362 --HELGGTFFQPTILCDVTPQMLVAREETFGPVAPIFKFTTDAEAIRMANDTEFGLASYF 419 Query: 429 ISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYLTVK 486 + D R R+++AL G++ IN AP+GG K SG GRE +G++ + +K Sbjct: 420 YTRDIGRVWRVAEALEYGMVGINTGLVSTEIAPFGGVKESGIGREGSRYGIEEFCEIK 477 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: 637 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: 506 Length of database: 484 Length adjustment: 34 Effective length of query: 472 Effective length of database: 450 Effective search space: 212400 Effective search space used: 212400 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 24 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