Align succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)
to candidate WP_013459096.1 SULKU_RS01190 aldehyde dehydrogenase
Query= metacyc::MONOMER-20455 (480 letters) >NCBI__GCF_000183725.1:WP_013459096.1 Length = 471 Score = 251 bits (640), Expect = 5e-71 Identities = 163/468 (34%), Positives = 239/468 (51%), Gaps = 17/468 (3%) Query: 17 WLSALGGETQSI---FNPATGQLIGTVPMMGRQEARQAIAAANQALPAWRALPAKERSAR 73 W+ + TQS +P G+++ +ARQA+ A A + + +R A Sbjct: 6 WMGSRQVVTQSYNERLSPYDGRVVSRAAECSADDARQALIIAQNASKIAKKVALHQRCAW 65 Query: 74 LRAWFELMLEHQEELARLMTIEQGKPLAEARNEILYAASFVEWFAEEGKRVYG-----DV 128 L + E +EE AR++ E GKP+ AR E+ + AE + ++G D Sbjct: 66 LLDVASKLKEQREEFARVLCDEVGKPITYARIEVDRCIETITLSAETMRTMHGESINTDA 125 Query: 129 IPSPQADKRLLVIKQPVGVTAAITPWNFPSAMITRKAAPALAAGCTMVLKPAPQTPFSAL 188 +PS +A ++ GV AITP+NFP ++ K APAL AG +VLKP P+ P A Sbjct: 126 MPSGRA-AHAYWRREAAGVVVAITPFNFPLNLVAHKLAPALVAGNAVVLKPTPEAPLCAY 184 Query: 189 ALAAL-AQRAGIPAGVFNVVTGSAQEIGGEFTGNPIVRKLTFTGSTHIGRLLMAQCAHDV 247 LA L + +VV G A E+G G+ I R ++FTGS +G ++ + Sbjct: 185 KLAQLFIESPYATPDALSVVYGDA-EVGSALVGSDIPRVISFTGSVGVGNIITRSAG--I 241 Query: 248 KKMSLELGGNAPFIVFEDADLDKAAEGALIAKYRNNGQTCVCTNRIYVHDSVHDAFAGKL 307 KK+SLELGGNA + ADL+ AA I + N+GQ C+ RIYV SV+D FA K+ Sbjct: 242 KKISLELGGNAATYIDTSADLEYAAARCAIGAFVNSGQVCISLQRIYVDSSVYDEFALKM 301 Query: 308 KKAVEGLRVGNGLEDGVTVGPLINDAAVQKVRSHIADAVGKGASILAGGKPHALGGTFFE 367 +A L VG+ D +GPLIND A + S + A+ +GA L P G F Sbjct: 302 AEATSKLVVGSPYNDDTFLGPLINDEAASRAMSWVESAIEEGARALT---PPRCEGRIFY 358 Query: 368 PTILANVPHDALVAHEETFGPLAPLFRFRDEAEVVGRANDTEYGLAAYFYTENLGRIFRV 427 P ++A+V + EE F P+ L R + + R N++ YGL +T NL + Sbjct: 359 PCVMADVTESMKIVCEEVFAPIVSLVRVDGIDDAITRMNNSPYGLQFSVFTNNLSHATKA 418 Query: 428 AEALEYGMVGIN-CGAISNEVAPFGGVKASGLGREGSKYGIEEYLEIK 474 + L+ G V IN + ++ P+GGVK SG+GREG ++ IEE+ EIK Sbjct: 419 IDELDAGGVVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEFTEIK 466 Lambda K H 0.319 0.135 0.399 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: 519 Number of extensions: 22 Number of successful extensions: 6 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: 480 Length of database: 471 Length adjustment: 33 Effective length of query: 447 Effective length of database: 438 Effective search space: 195786 Effective search space used: 195786 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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