Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__BFirm:BPHYT_RS22430 Length = 486 Score = 217 bits (552), Expect = 9e-61 Identities = 143/442 (32%), Positives = 225/442 (50%), Gaps = 12/442 (2%) Query: 37 SPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLG 96 +P TGE IA++ + AE I+ A+ A+ AWR A +R ++R + + DL Sbjct: 35 NPATGETIATVPRMGTAETRRAIDTANAAWPAWRATTAKQRAVILRKWHDLMMENADDLA 94 Query: 97 RLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVG 156 ++++ E GK +E GE+Q ++ +++ G TI T R++ T P+GV Sbjct: 95 KILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRVNGDTIPTPASDKRIVVTKEPIGVCA 154 Query: 157 IISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLS 216 I+ +NFP A+ + AL G ++ KP+E TPL+ALA + ERA P G+ Sbjct: 155 AITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPLSALALAVLAERA-----GVPRGVF 209 Query: 217 QVLIGD-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCP 275 V+ G+ +AIG + +P V +S TGST +GR + + A + LELGGN IV Sbjct: 210 NVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQCAPTVKKVSLELGGNAPFIVFD 269 Query: 276 SADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAA 335 ADLD A+ +GQ C R +VH+ VYD +L+ A + + VG E Sbjct: 270 DADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVYDAFAEKLRVAVEQLKVGRGTEDGV 329 Query: 336 LVGPLVDKAAFDGMQKAIAEAKNHGG-AVTGGERVELGHENGYYVKPALVEMPKQEGPVL 394 GPL++ AA ++ I +A G VTGG+R LGH G++ L ++ Sbjct: 330 TQGPLINDAAVLKVESHIEDALAKGARIVTGGKRHALGH--GFFEPTVLADVTPAMKVAR 387 Query: 395 EETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNI 454 +ETF P+ + ++S + V+ N GL+S ++RD+ R A+ + G+ +N Sbjct: 388 DETFGPLAPLFRFSSDEEVIRLANDTEFGLASYFYSRDIGRVWR--VAEALEYGMVGINT 445 Query: 455 GTSGAEIGGAFGGEKETGGGRE 476 G E+ FGG K++G GRE Sbjct: 446 GLISNEV-APFGGVKQSGLGRE 466 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: 571 Number of extensions: 29 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: 510 Length of database: 486 Length adjustment: 34 Effective length of query: 476 Effective length of database: 452 Effective search space: 215152 Effective search space used: 215152 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