Align 2-aminomucoate semialdehyde dehydrogenase subunit (EC 1.2.1.32) (characterized)
to candidate WP_082115713.1 AAW01_RS11260 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= metacyc::MONOMER-13321 (542 letters) >NCBI__GCF_001010925.1:WP_082115713.1 Length = 1202 Score = 117 bits (293), Expect = 3e-30 Identities = 90/264 (34%), Positives = 124/264 (46%), Gaps = 27/264 (10%) Query: 29 LVAIVHEASRELVDEAVKSGHQALSGEWGRTTATQRVALLRRIADEMERRQGDFLAAEMA 88 +V V A E E+VK +A G W T+ +R L + AD +E R + L M Sbjct: 606 VVGHVSWAHEEGALESVKRAAEAFPG-WSSTSVHERAECLEKAADLLEDRMENLLGLIMR 664 Query: 89 DTGKPHSMASSIDVPRGIANFRTFADILATAPVDSHRLDLADGAYALNYSARKPLGVVGV 148 + GK P IA R D L + D DGA AL G V Sbjct: 665 EAGK--------SAPNAIAEVREAVDFLRYYAQQAR--DSLDGADAL--------GPVVC 706 Query: 149 ISPWNLPLLLMTWKVAPALACGNTVVVKPSEDTPGTATLLAEVMEAAGVPPGVFNLVHGF 208 ISPWN PL + +V+ ALA GNTV+ KP+E+TP A +M AGVP V LV G Sbjct: 707 ISPWNFPLAIFVGEVSAALAAGNTVLAKPAEETPLIAAQAIGIMHEAGVPEDVVQLVPGD 766 Query: 209 GPNSAGEFISSHPDISAITFTGESRTGTTIMRAAAE----GVKPVSF--ELGGKNAAIIF 262 G G + PDI +TFTG + I R AE G P+ F E GG+NA ++ Sbjct: 767 G--RIGAALVGSPDICGVTFTGSTEVAKIIQRQLAERLLPGGSPLPFIAETGGQNAMVVD 824 Query: 263 ADCDFDKMLDTMMRALFLNSGQVC 286 + ++++ ++ + F ++GQ C Sbjct: 825 SSALPEQVVRDVVASAFDSAGQRC 848 Lambda K H 0.319 0.135 0.423 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: 1113 Number of extensions: 60 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: 542 Length of database: 1202 Length adjustment: 41 Effective length of query: 501 Effective length of database: 1161 Effective search space: 581661 Effective search space used: 581661 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: 55 (25.8 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