Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate RR42_RS21760 RR42_RS21760 succinate-semialdehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Cup4G11:RR42_RS21760 Length = 482 Score = 223 bits (567), Expect = 2e-62 Identities = 151/452 (33%), Positives = 227/452 (50%), Gaps = 12/452 (2%) Query: 37 SPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLG 96 +P TGE++ + + A E IE A+ A AWR A +R L+R E L A + DL Sbjct: 31 NPATGERVGQVPLLGADETRQAIEAANRALPAWRARTAKERSALLRKWFELLLANQDDLA 90 Query: 97 RLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVG 156 R+++ E GK +E GE+ ++ +++YG TI R++ T P+GV Sbjct: 91 RIMTAEQGKPFAEARGEIGYAASFIEWFAEEGKRVYGETIPAPVSNQRIVVTKEPVGVCA 150 Query: 157 IISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLS 216 I+ +NFP A+ + A AL G +V KP+ +TPLTALA A+ ERA P G+ Sbjct: 151 AITPWNFPAAMITRKAGPALAAGCTMVVKPASQTPLTALAMVALAERA-----GIPAGVL 205 Query: 217 QVLIGD-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCP 275 V+ G AIG L +P V ++ TGST +GR + + A + +ELGGN IV Sbjct: 206 SVVTGSAAAIGGELSSNPLVRKLTFTGSTEVGRTLMAQTASTIKKVSMELGGNAPFIVFE 265 Query: 276 SADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAA 335 ADLD A+ AGQ C RL+VH VYD +L A +++ VGN +E Sbjct: 266 DADLDAAVEGAIVSKYRNAGQTCVCANRLYVHSKVYDAFAEKLVAAVRALKVGNGMEDGV 325 Query: 336 LVGPLVDKAAFDGMQKAIAEAKNHGGAV-TGGERVELGHENGYYVKPALVEMPKQEGPVL 394 +GPL+D A +++ I +A + G V GG+R LG ++ L ++ Sbjct: 326 RIGPLIDGKAVTKVEEHITDAISKGARVLQGGKRHALG--QSFFEPTVLADVTPGMLVAR 383 Query: 395 EETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNI 454 EETF P+ + ++ D V+A N GL+S + RD+ R ++ + G+ VN Sbjct: 384 EETFGPLAPLFRFETEDEVVAMANDTEFGLASYFYARDLGRVWR--VSERLEYGMVGVNT 441 Query: 455 GTSGAEIGGAFGGEKETGGGRESGSDAWKAYM 486 G E+ FGG K++G GRE + Y+ Sbjct: 442 GLISNEV-APFGGVKQSGVGREGSHYGIEDYL 472 Lambda K H 0.317 0.134 0.390 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: 512 Number of extensions: 25 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: 510 Length of database: 482 Length adjustment: 34 Effective length of query: 476 Effective length of database: 448 Effective search space: 213248 Effective search space used: 213248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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