Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 190 bits (482), Expect = 1e-52 Identities = 145/466 (31%), Positives = 223/466 (47%), Gaps = 36/466 (7%) Query: 3 ELFIDGAWVDGAGPVFASR-----NPGTNERVWEGASASADDVERAVASARRAFAAWSAL 57 + ++DGAWV P SR NP T + A ADD RA+ +A +AF AW+A Sbjct: 6 DFYVDGAWVK---PAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAAT 62 Query: 58 DLDARCTIVKRFAALLVERKEALATMIGRETGKPLW------EARTEVASMAAKVDISIT 111 L R I+ + A R + +A I E G PL +AR + + ++ T Sbjct: 63 PLAERLEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKT 122 Query: 112 AYHERTGEKRAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPS 171 ER G ++ P GVV++ P+N+P + + PAL AG +V KPS Sbjct: 123 YAFERR--------QGTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPS 174 Query: 172 ELAPGVARATVEIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLH 230 E AP AR EI +AG+PAGV N+V G+ + G L++H +D + TGS+ G+ + Sbjct: 175 EFAPYSARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVM 234 Query: 231 KQFGGRPEIVLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGA 290 ++ G ++LE+GG + ++ + D A+ HA+++ + GQ C R+ VP Sbjct: 235 RE-GAATIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHR 293 Query: 291 FGDRFVARLADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMK 350 D A++ ++I +DP+ MG + + R ++ + GA + Sbjct: 294 L-DEAEGLAAELCAQIKVG-DPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGP 351 Query: 351 QRDPALG---FVNAAILD-VTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSA 406 +R L FV + VT+ + EE FGP+ + Y DLDDA+A AND +GLS Sbjct: 352 ERPEGLDKGYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSG 411 Query: 407 GLLADDEQAWHTFRRAIRAGIVNWNRPTNGASS--AAPFGGAGRSG 450 + A D R +R G+V+ NGA S PFGG +SG Sbjct: 412 YVYAGDLDEARAVARRLRTGMVH----LNGALSHPGGPFGGIRQSG 453 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: 518 Number of extensions: 27 Number of successful extensions: 3 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: 479 Length adjustment: 34 Effective length of query: 453 Effective length of database: 445 Effective search space: 201585 Effective search space used: 201585 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