Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_086510804.1 BZY95_RS15485 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::C6KEM4 (506 letters) >NCBI__GCF_002151265.1:WP_086510804.1 Length = 481 Score = 324 bits (830), Expect = 5e-93 Identities = 190/491 (38%), Positives = 277/491 (56%), Gaps = 18/491 (3%) Query: 1 MAPPQTIPRRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAF 60 M+ P I FIGG WR+ RR V NPA T+ +P +A+D AVAAA A+ Sbjct: 1 MSLPADIFSDKAFIGGQWRDA--ERRFDVTNPANGETLASVPDLSADDARDAVAAAEAAW 58 Query: 61 SRDGGRQWSRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASGDMDDVAACF 120 W R RA LRA I + LA + TL+ GKPL E+ G++ A+ Sbjct: 59 PA-----WRRQTAKQRAALLRAWFDAIMAHQESLARMMTLEQGKPLAESRGEVAYGASFV 113 Query: 121 EYYADLAEALDGKQRSPISLPMENFKSYVL--KEPIGVVGLITPWNYPLLMATWKVAPAL 178 E+YA+ A+ + G+ +LP +L +EP+GVV ITPWN+PL M T K APAL Sbjct: 114 EFYAEQAKRMAGE-----TLPSHGADKRILVFREPVGVVAAITPWNFPLAMITRKCAPAL 168 Query: 179 AAGCTTILKPSELASVSCLELGAICMEIGLPPGVLNIITGLGP-EAGAPLSSHSHVDKVA 237 AAGC ++KP+E ++ L L + ++G P GVLN++T P E G L+S V KV+ Sbjct: 169 AAGCPVVIKPAEATPLTALALARLAEQVGFPAGVLNVVTASRPAEIGEVLTSDPRVRKVS 228 Query: 238 FTGSTETGKRIMTSAAQMVKPVSLELGGKSPLIVFDDIGDIDKAVEWTMFGIFANAGQVC 297 FTGST GKR++ A VK S+ELGG +P IVFDD D+D AVE + + N+GQ C Sbjct: 229 FTGSTAVGKRLLAQCAGTVKKASMELGGNAPFIVFDD-ADLDAAVEGAVASKYRNSGQTC 287 Query: 298 SATSRLLLHEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARS 357 T+RLL+ + + F+++L A +KV + L+EG G +I++ +K++ I+ A + Sbjct: 288 VCTNRLLVQSGVYEAFVEKLAARVAQLKVGNGLDEGVVQGPLINQAAVDKVQSHIADALA 347 Query: 358 EGATILYGGGRPQHLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELA 417 +GA ++ GG H G F +PT++ DV+ M++ +EE FGP+ V F +D +A+ +A Sbjct: 348 KGARLVCGG--EPHALGGTFFQPTVVADVTDEMRVAREETFGPLAPVFRFDSDEQAIAMA 405 Query: 418 NDTHYGLAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEW 477 N T +GLA + D R + + L G++ +N AP+GG K SG GRE Sbjct: 406 NATEFGLAAYFYARDYRRIWHVMEGLEYGMVAVNEGILSTELAPFGGVKESGLGREGSHH 465 Query: 478 GLDNYLTVKQV 488 GLD + +K V Sbjct: 466 GLDEFTELKYV 476 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: 609 Number of extensions: 35 Number of successful extensions: 8 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: 481 Length adjustment: 34 Effective length of query: 472 Effective length of database: 447 Effective search space: 210984 Effective search space used: 210984 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