Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_090447986.1 BLS63_RS22155 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_900100495.1:WP_090447986.1 Length = 502 Score = 374 bits (959), Expect = e-108 Identities = 210/482 (43%), Positives = 295/482 (61%), Gaps = 6/482 (1%) Query: 16 LAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDW 75 L+ ++FI G + A++ + E ++P T+ L +I G D+DRA+ AARG F+ G W Sbjct: 22 LSKAQKMFIGGAWLDASDGGSAEVIEPSTEGLLTRIPMGTVADLDRAVQAARGQFDGGAW 81 Query: 76 SLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAI 135 P +R+ +L++LADL+EA+A ELA +E++D GK + + DI G+ R++A Sbjct: 82 RQLKPLQRERLLHRLADLLEANAAELAEIESIDMGKSLVQAGAVDIQGSIDTFRYFAGWA 141 Query: 136 DKVYGEVATTS--SHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPS 193 K++G S + LA +EPVGV+ IVPWNFPL WKLG ALA G SV++KP+ Sbjct: 142 SKIHGRSVEPSLPGNYLAYTRKEPVGVVGVIVPWNFPLQTLAWKLGAALAVGCSVVVKPA 201 Query: 194 EKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLL 253 E + LSA+R A L ++AG+PDGV+N+VTG G G A++ H ID ++FTGST G + Sbjct: 202 ELTSLSALRFAELVQQAGIPDGVVNIVTGRGSVVGAAMASHPGIDKLSFTGSTPVGCSVG 261 Query: 254 KDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEES 313 K A MKR+ LE GGKS IVFAD DL+ AA A A G+F+N GQVC AGTR ++ S Sbjct: 262 K-AALEQMKRLTLELGGKSPVIVFADA-DLKAAAQAVANGVFFNSGQVCDAGTRAYIQRS 319 Query: 314 IADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA 373 I +FL L + + LDP + L+ + V +I G+++G L G A Sbjct: 320 IYPQFLRELAAYTASLKIAPGLDPDCFISPLVSRQQQERVLGYIAAGKAEGAELYYGGEA 379 Query: 374 --GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 G + PTIF + + + +EEIFGPVLV F EE+AL LANDS +GL AA+++ Sbjct: 380 VEGPGYFVQPTIFANCRNDMRIVQEEIFGPVLVTAPFDDEEEALALANDSPFGLAAALYS 439 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 DL R H + RL+AGSV+VN ++ D +PFGGYKQSG G+D L+ E K +WI Sbjct: 440 NDLGRVHSLIPRLRAGSVYVNAHSTIDPAMPFGGYKQSGYGKDLGAEQLDYLLETKAVWI 499 Query: 492 SL 493 +L Sbjct: 500 TL 501 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: 574 Number of extensions: 24 Number of successful extensions: 5 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: 502 Length adjustment: 34 Effective length of query: 461 Effective length of database: 468 Effective search space: 215748 Effective search space used: 215748 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