Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate PfGW456L13_5044 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5044 Length = 481 Score = 214 bits (546), Expect = 4e-60 Identities = 142/447 (31%), Positives = 222/447 (49%), Gaps = 10/447 (2%) Query: 42 EKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGRLVSI 101 + I A+ I+ A AF AW R + + +G E+ A + +LG L++ Sbjct: 32 DAIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARHDSLDKVGTEILARREELGTLLAR 91 Query: 102 EAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGIISAF 161 E GK E +GEV +I F G +L G + + RPG + T LGVVG+I+ + Sbjct: 92 EEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPW 151 Query: 162 NFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIG 221 NFP+A+ +W A AL G+ VV KP++ P A A I+ RA P G+ +++G Sbjct: 152 NFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALAEIISRA-----GFPAGVFNLVMG 206 Query: 222 D-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLD 280 R +G+ LV PKV +S TGS +GR++ R A+ LE+GG N I+ ADL Sbjct: 207 SGRVVGDALVHSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQLEMGGKNPQIILDDADLK 266 Query: 281 MALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPL 340 A+ A + GQRCT R V ++DQ V + + +S+ VG+ L++ +GP+ Sbjct: 267 QAVELSVQSAFYSTGQRCTASSRFIVTAGIHDQFVEAMAERMKSIKVGHALKAGTDIGPV 326 Query: 341 VDKAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALVEMPKQEGPV-LEETFA 399 V +A + K I ++ G + G + GY++ P L + + EE F Sbjct: 327 VSQAQLEQDMKYIDIGQSEGARLVSGGGLVTCDTEGYFLAPTLFADSEASMRISQEEIFG 386 Query: 400 PILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGA 459 P+ +++ +D++A LA N GLS+ I T ++ + F S G+ VN+ T+G Sbjct: 387 PVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHF--KRHSQAGMVMVNLPTAGV 444 Query: 460 EIGGAFGGEKETG-GGRESGSDAWKAY 485 + FGG K + G RE G A + Y Sbjct: 445 DYHVPFGGRKGSSYGSREQGRYAQEFY 471 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: 518 Number of extensions: 25 Number of successful extensions: 5 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: 481 Length adjustment: 34 Effective length of query: 476 Effective length of database: 447 Effective search space: 212772 Effective search space used: 212772 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