Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011912900.1 PST_RS08835 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000013785.1:WP_011912900.1 Length = 490 Score = 355 bits (911), Expect = e-102 Identities = 191/481 (39%), Positives = 283/481 (58%), Gaps = 13/481 (2%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGD--WSLS 78 +L+I+G Y A+ N+TFE+++P LA++A + D++RA+ +A E+G W+ Sbjct: 8 QLYIHGAYVDASSNQTFESINPANGEVLAEVAEAGAADLERAVESA----EQGQRIWAAL 63 Query: 79 SPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKV 138 + +R ++ + DL+ +ELALLETLDTGKP+ + DI A + +YA + Sbjct: 64 TGIERARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIITGADVLEYYAGLAPAI 123 Query: 139 YGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198 GE REP+GV+A I WN+P+ + WK PALAAGN++I KPSE +PL Sbjct: 124 EGEQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTPL 183 Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258 SA+RLA + EAGLPDGV NV+TG G G ++ H I ++FTG TGK+++ A Sbjct: 184 SALRLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAAG 243 Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 S++K V +E GGKS IV D DL +AA F++ GQVC GTR+ + + F Sbjct: 244 SSLKDVTMELGGKSPLIVCEDA-DLDRAADIAVMANFFSSGQVCTNGTRVFIPAGLKASF 302 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA----- 373 A L ++ Q + G P AT G L+ AH D V +I +G++ G +L G Sbjct: 303 EAKLLERVQRVRLGDPQQEATNFGPLVSFAHMDKVLDYIAQGKAAGARILCGGERVTEGE 362 Query: 374 -GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTR 432 A + PTIF D + S+ REEIFGPVL + + E++A++ AND++YGL A V T Sbjct: 363 YARGAFVAPTIFSDCSDDMSIVREEIFGPVLSLLEYQGEDEAIRRANDTEYGLAAGVVTP 422 Query: 433 DLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492 DL+RAHR+ RL+AG ++N + + +P GGYKQSG GR+ + +L +T +K++ + Sbjct: 423 DLARAHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQVE 482 Query: 493 L 493 L Sbjct: 483 L 483 Lambda K H 0.317 0.133 0.389 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: 572 Number of extensions: 17 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: 495 Length of database: 490 Length adjustment: 34 Effective length of query: 461 Effective length of database: 456 Effective search space: 210216 Effective search space used: 210216 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