Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 164 bits (415), Expect = 7e-45 Identities = 150/489 (30%), Positives = 234/489 (47%), Gaps = 30/489 (6%) Query: 10 VASEAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFR-- 67 +A + A++D G + +G + SP G+ + + A + + A AF Sbjct: 17 LAPPSQAVID--GDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDG 74 Query: 68 AWR-LVPAPKRGELVRLLGEELRAFKAD-LGRLVSIEAGKIPSEGLG-EVQEMIDICDFA 124 WR P K+ L RL EL AD L L S++ GK S+ ++ I+ C + Sbjct: 75 RWRDQGPRQKKAVLFRLA--ELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWY 132 Query: 125 VGLSRQLYGLTIATERPGHRMMETWH-PLGVVGIISAFNFPVAVWSWNAALALVCGDAVV 183 ++YG + T P R+ H PLGV+G I +NFP+ + W A AL G++VV Sbjct: 133 AEALDKVYG-EVGTS-PADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVV 190 Query: 184 WKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIGDRAI-GEVLVDHPKVPLVSATG 242 KP+E++PLTAL A+ A P G+ V+ G + GE L V +++ TG Sbjct: 191 LKPAEQSPLTALKLGALALEA-----GLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTG 245 Query: 243 STRMGREVGPRLAK-RFARAILELGGNNAGIV---CPSADLDMALRAIAFGAMGTAGQRC 298 S +GR + A+ R LELGG + IV CP DL+ A +A A+G G+ C Sbjct: 246 SGPVGRRLMEYSARSNLKRVSLELGGKSPQIVFADCP--DLEAAAQAAAWGVFYNQGEVC 303 Query: 299 TTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKN 358 T RL V + D + R+ + + + VG+PL+ + G +V + + IA A + Sbjct: 304 TAASRLLVEAPIKDAFLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADS 363 Query: 359 HGG-AVTGGERVELGHENGYYVKPALVEMPKQEGPVL-EETFAPILYVMKYSDFDAVLAE 416 G V GG+RV G+YV+P + + + + + EE F P+L VM +S D + Sbjct: 364 QGARRVLGGQRVR-QEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRL 422 Query: 417 HNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRE 476 N GL++ ++T D+ ++ R A G+ VN G +I FGG K++G GR+ Sbjct: 423 ANDTVYGLAAGLWTADVSKALR--GARRLKAGLVWVN-GWDACDITMPFGGFKQSGFGRD 479 Query: 477 SGSDAWKAY 485 A Y Sbjct: 480 RSLHALHKY 488 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: 580 Number of extensions: 37 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: 499 Length adjustment: 34 Effective length of query: 476 Effective length of database: 465 Effective search space: 221340 Effective search space used: 221340 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