Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= curated2:Q87L22 (485 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 160 bits (406), Expect = 7e-44 Identities = 128/420 (30%), Positives = 198/420 (47%), Gaps = 17/420 (4%) Query: 20 LSPYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAEREAIVLAFAEKVKENSEKI 79 ++P Q+V+ + AT +VD AVAAA+ AF W+K P R I L + + ++EN ++ Sbjct: 28 VNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTPIGTRARIFLKYQQLIRENMSEL 87 Query: 80 AEVIAKETGKPIWETRTEAAAMAGKIAISIRAYHDRTGE-ATREAAGNQIVLRHRPLGVM 138 A ++ E GK + + + + + + + GE A A G +PLGV Sbjct: 88 AHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLGELANNVANGVDTYTLMQPLGVC 147 Query: 139 AVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTGELAMKLWEEAGLPKGVINLVQ 198 A P+NFP +P A+ GNT V KPSEQ P ++L EAG+PKGV+N+V Sbjct: 148 AGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLVELALEAGIPKGVLNVVH 207 Query: 199 GAKETGIALADAKGIDGILFTGSANTG-HILHRQFAGQPGKMLALEMGGNNPMVISDNYG 257 G +E A+ D I + F GS G H+ +R A GK + MG N V+ + Sbjct: 208 GGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNR--ASLAGKRVQCMMGAKNHAVVLPD-A 264 Query: 258 DLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALITKLVEATKNIRMDQPFAEPAP 317 + + T+ ++ +AF +AGQRC A L V GE + + LV K +++ + Sbjct: 265 NKEQTLNAMVGAAFGAAGQRCMAASTL-VLVGE-ARSWVPDLVAKAKTLKVSAG-SVAGT 321 Query: 318 FMGPQISVAAAKFI-------LDAQANLQSLGGESLIEAKAGEAAFVSPGIID-VTNIAE 369 +GP IS +A + + L+ A L G ++ + FV P I VT Sbjct: 322 DVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDG-FEKGNFVGPTIFSGVTTDMR 380 Query: 370 LPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSAGLVSTDDQEWEYFVDHIRAGIVNRN 429 + EE FGP+L ++ E L+ A+ L N G + + F + I G V N Sbjct: 381 IYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAAARKFQEDIDVGQVGIN 440 Lambda K H 0.316 0.134 0.397 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: 565 Number of extensions: 33 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: 485 Length of database: 501 Length adjustment: 34 Effective length of query: 451 Effective length of database: 467 Effective search space: 210617 Effective search space used: 210617 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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