Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Marino:GFF4092 Length = 486 Score = 295 bits (754), Expect = 3e-84 Identities = 171/478 (35%), Positives = 262/478 (54%), Gaps = 11/478 (2%) Query: 14 YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPA-WRALTAKER 72 Y++G +V + +G+ NPA G++I V + G E A++AA AL W +T ++R Sbjct: 7 YINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALRGPWGKMTLEQR 66 Query: 73 ANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTI 131 L + D + D+ ++ GKP + A +I A+ + F + K + ++ Sbjct: 67 TAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADMIKNVPTESF 126 Query: 132 PGHQPDKRIIV---IKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYS 188 PD + +++P GV I+PWN P ++T K GPALA G T+V+KP+ +TP + Sbjct: 127 EMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPTT 186 Query: 189 ALALAELAERAGIPKGVFSVVTGSAGE-VGGELTSNPIVRKLTFTGSTEIGRQLMAECAQ 247 L E+ + AG+P GV++VV G G+ G LT +P V TFTG T G +M A+ Sbjct: 187 TALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEVIMKAAAK 246 Query: 248 DIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVD 307 I+ +SLELGG +VF D D++ A+EG + S + N GQ C+ R+YV+ ++D FV Sbjct: 247 GIRDISLELGGKNAGLVFADCDMEKAIEGTMRSAFANCGQVCLGTERVYVERSIFDEFVG 306 Query: 308 KLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGG-----KPHA 362 +LK A L IG +A GPL+ K KV + AV GA VV+GG Sbjct: 307 RLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGGVPDMPAEL 366 Query: 363 LGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARD 422 GG + EPTI +P ++ V DE FGP + F E E I ++N +GLAS ++ + Sbjct: 367 AGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWSEN 426 Query: 423 LARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 + R RVA Q+E G++ +N+ + + PFGG K SG+GREG + +E Y E+K +C+ Sbjct: 427 ITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGVGREGGVHSLEFYTEMKNICV 484 Lambda K H 0.317 0.135 0.391 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: 612 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: 483 Length of database: 486 Length adjustment: 34 Effective length of query: 449 Effective length of database: 452 Effective search space: 202948 Effective search space used: 202948 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