Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF4637 PS417_23725 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::P07275 (575 letters) >FitnessBrowser__WCS417:GFF4637 Length = 505 Score = 130 bits (328), Expect = 1e-34 Identities = 130/420 (30%), Positives = 193/420 (45%), Gaps = 42/420 (10%) Query: 60 EVPLVINGERIYDNNERALFPQTNPANHQQVLANVTQATEKDVMNAVKAAKDAKKDWYNL 119 +V L+INGE + ++ NPA Q+VLA V AT +V A+ AA A + W Sbjct: 11 QVKLLINGEWV-ESKTTEWQDIVNPAT-QEVLAKVPFATADEVNAAIDAAHRAFQTWKLT 68 Query: 120 PFYDRSAIFLKAADLISTKYRYDMLAATMLG--QGKNVYQAEIDCITELSDFFRYYVKYA 177 P R I LK LI + A +L QGK + AE D L V++A Sbjct: 69 PIGARMRIMLKLQALIR---EHSKRIAVVLSNEQGKTIADAEGDIFRGLE-----VVEHA 120 Query: 178 SDLYAQQPVESADGTWNKAEYRPLE---GFVYAVSPFNFTAIAANLIGAPALM-GNTVVW 233 + Q E ++ + L G ++PFNF A+ + A+ GNT V Sbjct: 121 CSIGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180 Query: 234 KPSQTAALSNYLLMTVLEEAGLPKGVINFIPGDPVQVTDQVLADKDFGALHFTGSTNVFK 293 KPS+ LS LL+ + EAG+P GV+N + G V D + KD A+ F GST V Sbjct: 181 KPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGK-DVVDALCTHKDIKAVSFVGSTAVGT 239 Query: 294 SLYGKIQSGVVEGKYRDYPRIIGETGGKNFHLVHPSANISHAVLSTIRGTFEFQGQKCSA 353 +Y + GK+ R+ G KN +V P AN H + + + F GQ+C A Sbjct: 240 HVYD------LAGKHG--KRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMA 291 Query: 354 ASRLYLPESKSEEFLSDMFGILQSQNVVPMNTSASPISGGNLRGFMGPVIHEQSFDKLVK 413 S + L S+++L D+ + Q V +G +GPVI +++ ++++ Sbjct: 292 TSVVVL-VGASKQWLPDLKALAQKLKV---------NAGSEAGTDVGPVISKRAKARILE 341 Query: 414 VIED-AKKDPELEILYGGQYDK----SQGWFVGPTVIKAKRPDHPYMSTEFFGPILTVYE 468 +IE K+ +LE+ G+ K QG FVGPT+ P + E FGP+L V E Sbjct: 342 LIESGVKEGAKLEL--DGRDIKVPGFEQGNFVGPTLFSGVTPSMQIYTQEIFGPVLVVLE 399 Lambda K H 0.318 0.135 0.401 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: 605 Number of extensions: 31 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: 575 Length of database: 505 Length adjustment: 35 Effective length of query: 540 Effective length of database: 470 Effective search space: 253800 Effective search space used: 253800 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 17 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