Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012406034.1 BPHY_RS34150 aldehyde dehydrogenase
Query= BRENDA::Q4DRT8 (561 letters) >NCBI__GCF_000020045.1:WP_012406034.1 Length = 497 Score = 143 bits (361), Expect = 1e-38 Identities = 132/440 (30%), Positives = 199/440 (45%), Gaps = 32/440 (7%) Query: 90 KAIDTALQASRE------WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKSPFQ 143 K ID A+ A+RE WS+ + R A+ L A LI EL L K + Sbjct: 55 KDIDRAVAAAREAFESGVWSKAAPAQRKAVLLRLAQLIEDN-TEELALLEALEAGKPISE 113 Query: 144 AEIDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEGFVSTIAPFNFAAI 203 I ES +R+ + Y LSPS V + + P+ G V + P+NF A+ Sbjct: 114 CLGLDIPESAACIRWHAEVTDKRY--DALSPSGAGVVSMITREPI-GVVGAVLPWNFPAL 170 Query: 204 AANLVACPAL-MGNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEPDVMTNFVN 262 PAL +GN V+ KP+ LS + + +AG+PAGV + + + + Sbjct: 171 MLAWKIGPALSVGNSVIVKPAEQTSLSTLRIADLALQAGVPAGVFSVVTGFGESAGQALG 230 Query: 263 SHRDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHPS-ADLKLAA 321 H D+ VAFTGST+ + + R N+ R+ E GGK+ +V P A+L A Sbjct: 231 RHADVDLVAFTGSTE-----TGKRFLRYSADTNLKRVVLECGGKNPQVVLPDVANLDAVA 285 Query: 322 ALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKSFMCAVIDE 381 V AF G+ CSA SR+ P S L + V E K G P D + ++I++ Sbjct: 286 EQAVAAAFWNMGENCSAGSRILVPSSLKASLLEKVQAVLEGWKTGDPLDPDVKLGSLIEQ 345 Query: 382 TAFERNKKYIDIAKSSPSTYSVIAGGGYDKTE--GWFVQPTIVESKDSQAQLMHEEIFGP 439 F++ +I+ AK+ + V+ GG +T+ GWFV+PTI ++ + +E+FGP Sbjct: 346 KHFDKVLGHIEQAKAEGA--RVVCGGKAARTDSGGWFVEPTIFDNVTPDMSIARDEVFGP 403 Query: 440 ILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAAGNYYIN 499 ++ Y D D + N T Y L S++ + + A R AG +N Sbjct: 404 VVCFIEYADI-----DDAVRIAN-DTCYGLAASLWTDN---VNHAHKVAARIRAGTVTVN 454 Query: 500 DKCTGAVVGQQPFGGARASG 519 C G PFGG + SG Sbjct: 455 --CFGEGDLSTPFGGFKQSG 472 Lambda K H 0.320 0.133 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: 591 Number of extensions: 28 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: 561 Length of database: 497 Length adjustment: 35 Effective length of query: 526 Effective length of database: 462 Effective search space: 243012 Effective search space used: 243012 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 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