Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_010961010.1 MCA_RS08650 NAD-dependent succinate-semialdehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_000008325.1:WP_010961010.1 Length = 491 Score = 215 bits (548), Expect = 3e-60 Identities = 145/452 (32%), Positives = 225/452 (49%), Gaps = 14/452 (3%) Query: 38 PVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGR 97 P TG +A + + AAE I A+ A+ WR A +R ++R E + + DL R Sbjct: 37 PATGRALADVPAMGAAETMRAIAAAEHAWTGWRGKTAKERAAVLRRWYELILSHTEDLAR 96 Query: 98 LVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGI 157 +++ E GK +E E+ ++ + + YG TI + P R++ P+GV Sbjct: 97 ILTAEQGKPLTEARNEIGYAAGFVEWFAEEAGRAYGETIPSPVPDKRLLVIRQPIGVCAA 156 Query: 158 ISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQ 217 I+ +NFP A+ + A AL G VV KP+E+TPLTALA + +A P G+ Sbjct: 157 ITPWNFPAAMITRKIAPALAAGCTVVVKPAEQTPLTALALADLAVQA-----GFPPGVIN 211 Query: 218 VLIGD-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPS 276 V+ GD AIG L +P + +S TGST +GR + + A + LELGGN IV Sbjct: 212 VVTGDPEAIGGELTSNPLIRKLSFTGSTEVGRLLMAQCAATVKKISLELGGNAPFIVFED 271 Query: 277 ADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAAL 336 ADLD A+ GQ C R + +S+YD RL + + VGN L+ + Sbjct: 272 ADLDAAVEGALLSKYRNTGQTCVCTNRFLIQDSIYDAFAERLAAKVRRLEVGNGLDEGVV 331 Query: 337 VGPLVDKAAFDGMQKAIAEAKNHGGAV-TGGERVELGHENGYYVKP-ALVEMPKQEGPVL 394 GPL+D+ A +++ IA+A + G V GG R LG G + +P LV++ + Sbjct: 332 QGPLIDEQALAKVERHIADALDRGARVLAGGGRHPLG---GRFFQPTVLVDVTPEMLCTR 388 Query: 395 EETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNI 454 EETF P+ ++++ + LA NA GL++ +TRD+ + F + + G+ +N Sbjct: 389 EETFGPVAPLLRFGSEEEALAIANATEYGLAAYFYTRDL--ARAFRVGEALEYGMVGINT 446 Query: 455 GTSGAEIGGAFGGEKETGGGRESGSDAWKAYM 486 G ++ FGG K++G GRE Y+ Sbjct: 447 GMLSYDV-APFGGVKQSGIGREGSHHGMDEYL 477 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: 573 Number of extensions: 32 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: 491 Length adjustment: 34 Effective length of query: 476 Effective length of database: 457 Effective search space: 217532 Effective search space used: 217532 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 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