Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_050465948.1 AKL27_RS26725 carnitine dehydratase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_001189915.1:WP_050465948.1 Length = 493 Score = 255 bits (652), Expect = 2e-72 Identities = 171/486 (35%), Positives = 248/486 (51%), Gaps = 20/486 (4%) Query: 36 RHYPLYIGGEWVD--TKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFK-TWKD 92 + Y L+I EWVD + + SL+P + E +A K + E A+EAA A + W Sbjct: 3 QRYQLFINNEWVDPLSGQWFDSLDPFS-GEPWAEVPRANKDDVERAVEAASAAMEGPWGK 61 Query: 93 WPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRY 152 DR LL K +L+ + L + GK E + V + YY A + Sbjct: 62 MSATDRGMLLHKLGSLIEKHADTLTLAESRDNGKLKSEVAGQVRYMAKYFYYYGGLADKI 121 Query: 153 RYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDA 212 + AV + P N + Y P+G I PWN + + + + GNT+IAKP+E Sbjct: 122 Q-GAVIPMDKPKVFNYTRYEPMGVVATITPWNSSLLLTAWKVAPALCAGNTIIAKPSEHT 180 Query: 213 VVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAA 272 V ++ ++F EAGFPPGV N + G G EVG LV HP+ I FTG E G K+ Sbjct: 181 SVSLLELAKLFVEAGFPPGVFNVITGFGGEVGEPLVTHPKVPRIAFTGGDEGGRKVN--- 237 Query: 273 GRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQ 332 G FKR +E GGK I+ + AD AA GV+ + GQ C A SRL+L + Sbjct: 238 ---VLGAQHFKRVSLELGGKSPHIIFDDADLTRAANGVITGIFSAGGQTCMAGSRLLLQE 294 Query: 333 GAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGK 390 ++ +ER++ A + +G P + +GPV + Q KV+ YI I KNEG + V GG Sbjct: 295 SIHDEFVERLVAIASKAKLGDPTLPDVQVGPVATRPQFDKVMEYIAIAKNEGARCVFGGN 354 Query: 391 RLEGEGY----FIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLT 446 GEG+ F+ PT+F +V RIAQEE+FGPVLSVI+ KD +A+ +AND +GL Sbjct: 355 ARTGEGFGAGQFVEPTIFVDVDNSMRIAQEEVFGPVLSVIKFKDEEDAIRIANDIRFGLA 414 Query: 447 GGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLF 506 GV++ G ++ N + + PFGG+K SGT + G ++ ++ + Sbjct: 415 SGVWTTSLHRAMLMTSRIKAGTVWVNNYRSTSF--TTPFGGYKDSGT-GREGGIEAVKEY 471 Query: 507 LEMKAV 512 LE K+V Sbjct: 472 LETKSV 477 Lambda K H 0.319 0.137 0.403 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: 37 Number of successful extensions: 6 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: 516 Length of database: 493 Length adjustment: 34 Effective length of query: 482 Effective length of database: 459 Effective search space: 221238 Effective search space used: 221238 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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