Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 204 bits (520), Expect = 5e-57 Identities = 157/477 (32%), Positives = 234/477 (49%), Gaps = 27/477 (5%) Query: 22 GVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAF--RAWRLVPAPKRGE 79 GV+ +G +P P T +A AA+ A + A AF WR + R + Sbjct: 28 GVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADREK 87 Query: 80 LVRLLGEELRAFKADLGRLVSIEAGKIPSEGLG---EVQEMIDICDFAVGLSRQLYGLTI 136 L+ L E + +L L ++++GK+ +G+ +VQ + + G + +L G T+ Sbjct: 88 LLFRLSELIERHADELSALETLQSGKL--QGIARAIDVQAGAEFVRYMAGWATKLEGQTL 145 Query: 137 --ATERPGHRMMETWH--PLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPL 192 + PG + + P+GVVG I +NFP+A+ W A AL G VV KPSE TPL Sbjct: 146 DNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPL 205 Query: 193 TALACQAI-LERAIARFGDAPEGLSQVLIGDRAI-GEVLVDHPKVPLVSATGSTRMGREV 250 TAL + LE I PEG+ V+ G A G L+ HP V +S TGST +G+ V Sbjct: 206 TALRLAHLALEAGI------PEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVV 259 Query: 251 GPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESV 310 G + AR LELGG + +V AD + IA G GQ CT RL VH S+ Sbjct: 260 GHAAVENMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSL 319 Query: 311 YDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGA-VTGGERV 369 Y +++ L Q + +G+ ++A GPL KA F + IA AK G V GGERV Sbjct: 320 YRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERV 379 Query: 370 ELGHENGYYVKPAL-VEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSI 428 H+ G +V+P + + Q V EE F P+L V + D + +A N GL++S+ Sbjct: 380 ---HDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASL 436 Query: 429 FTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAY 485 +T+ + + R + G+ VN + + G GG K++G GR+ G A + + Sbjct: 437 WTQSLSHAHRIVPR--LQAGVVWVN-AHNVLDAGLPLGGIKQSGTGRDLGRAAVEGF 490 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: 575 Number of extensions: 34 Number of successful extensions: 7 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: 500 Length adjustment: 34 Effective length of query: 476 Effective length of database: 466 Effective search space: 221816 Effective search space used: 221816 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