Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_009562902.1 RSPH17029_RS04350 betaine-aldehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >NCBI__GCF_000015985.1:WP_009562902.1 Length = 483 Score = 327 bits (838), Expect = 6e-94 Identities = 181/469 (38%), Positives = 273/469 (58%), Gaps = 4/469 (0%) Query: 15 INGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERAT 74 ++G L+ G I V PA G+++ + + AA+ + RA AW A+ ERA Sbjct: 11 VDGRPLEDETGAPIPVIYPATGEEIARLHEATPAVIEAALASGARAQAAWAAMRPVERAR 70 Query: 75 ILRNWFNLMMEHQDDLARLMTLEQGKPLAEAK-GEISYAASFIEWFAEEGKRIYGDTIPG 133 ILR +L+ ++L+ L TL+ GKPL E + + A +E+FA + G+T+P Sbjct: 71 ILRRASDLIRARNEELSLLETLDTGKPLQETLVADWASGADALEFFAGLAPAVTGETVPL 130 Query: 134 HQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALA 193 Q + I++P+G+ I WN+P+ + KA PALA G MV KP+ TP AL LA Sbjct: 131 GQ--DFVYTIREPLGLCVGIGAWNYPSQIACWKAAPALALGNAMVFKPSEVTPLGALKLA 188 Query: 194 ELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCAKDIKKVS 253 E+ I AG+P G+FNVV G GAVG L ++ V K+S TGS GR++ A+ ++ V+ Sbjct: 189 EILIEAGLPPGLFNVVQGR-GAVGAALVTDSRVAKVSLTGSVPTGRRVYAAAAEGVRHVT 247 Query: 254 LELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAV 313 +ELGG +P IVFDDADL+ A+ A+ F +AGQ C R++VQ G+ + F +L + Sbjct: 248 MELGGKSPLIVFDDADLESAIGAAMLGNFYSAGQICSNGTRVFVQKGIKEAFLARLAERA 307 Query: 314 SKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGGNFFQPTIL 373 + +GD LD V +GPL+ + + KV +I A +G R+VCGG+A G + QPT+ Sbjct: 308 DAIRMGDPLDPEVQMGPLVSQAQLEKVLAYIEKARAEGGRLVCGGEASVSPGCYVQPTVF 367 Query: 374 VDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEAL 433 DV +++EE FGP+ + F+ E + IA+AN T+FGLAA + DL+R RV L Sbjct: 368 ADVTDAMTLAREEVFGPVMAVLDFETEEEAIARANATDFGLAAGVFTADLTRAHRVVAQL 427 Query: 434 EYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIGL 482 + G IN ++ APFGG+K SG+GRE + +E Y ++K + +G+ Sbjct: 428 QAGTCWINAYNLTPVEAPFGGVKLSGVGRENGRAAVEHYTQVKSVYVGM 476 Lambda K H 0.318 0.135 0.395 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: 603 Number of extensions: 22 Number of successful extensions: 3 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: 482 Length of database: 483 Length adjustment: 34 Effective length of query: 448 Effective length of database: 449 Effective search space: 201152 Effective search space used: 201152 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 Apr 10 2024. 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