Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 227 bits (579), Expect = 6e-64 Identities = 172/471 (36%), Positives = 226/471 (47%), Gaps = 22/471 (4%) Query: 6 IDGAWVDGAGPVFASRNPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 I GAW DG + + NP T + + + A AS + AVA+A AF AWS R Sbjct: 39 IGGAWTDGVR-TYQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRFD 97 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 I+ ++ RK L ++ RE GK L EA EV AA GE + Sbjct: 98 ILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGGEVMPSV 157 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 GV + + P G + + P+NFP +P I PAL GN VVFKP+E+ PG A A + Sbjct: 158 RPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWALAD 217 Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I AGLPAGV NLV G D G L +I G+ FTGS TG + R V Sbjct: 218 ILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPRGAKV-Q 276 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 LEMGG NP VV + D++ AV AI S F S GQRCT + R++V G DRFVA A V Sbjct: 277 LEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEG-IHDRFVA--AMV 333 Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEM--------KQRDP 354 T V DA G I R +A +G+G ++ K D Sbjct: 334 EKMKTLKVDDARK---AGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADG 390 Query: 355 ALGFV--NAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADD 412 A GF A + T + EE FGP+ ++R + ++A+A ANDT FGL++G+ Sbjct: 391 APGFYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTS 450 Query: 413 EQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSG-NHRPSAYYAADY 462 + F+R +AG+V N PT G PFGG S R YAA++ Sbjct: 451 LKHATHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKSSSYGPREQGRYAAEF 501 Lambda K H 0.320 0.134 0.402 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: 613 Number of extensions: 28 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: 487 Length of database: 512 Length adjustment: 34 Effective length of query: 453 Effective length of database: 478 Effective search space: 216534 Effective search space used: 216534 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 (21.8 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