Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1480 Length = 486 Score = 379 bits (972), Expect = e-109 Identities = 200/462 (43%), Positives = 273/462 (59%) Query: 13 IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72 IDG+WVDA +G T+ V NPA G IG + +AG A A+AAA F W+ A +RA Sbjct: 18 IDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDRTAEDRAR 77 Query: 73 TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132 +R+ L+ + + +A +MT EQGKPL EAR E+ AA IEWFA+E RR+YG ++P Sbjct: 78 ILRRWFELMLQHQEDLALIMTSEQGKPLAEARGEIAYAASYIEWFAEEARRIYGEVIPSP 137 Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192 L + V +EPVG AA TPWNFP + RK++ ALA GC+ +VK +TP S A+ Sbjct: 138 WLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQTPLSALAMAE 197 Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252 AGVPAGV ++ GD I + L PV+RK+TFTGST +G+ LA+ +K+ ++ Sbjct: 198 LAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQCAPTLKKMSL 257 Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312 ELGG+AP IV EDAD+ AV A +K+RN GQ C+ R LV + + D F L + Sbjct: 258 ELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDAFAEKLARTVA 317 Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372 LKVG+GLEEG G L + LT + +++ +A+ GA + TGG R G F+ PT++A Sbjct: 318 ALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRRHALGGTFYEPTILA 377 Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432 ++ D + E FGPVA + F EAI AN FGLA Y ++R V ++ L+ Sbjct: 378 DITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDVGRVWRVSGALQ 437 Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 GM+ IN PFGGVK SG G EG +E Y+ TK Sbjct: 438 YGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTK 479 Lambda K H 0.318 0.134 0.393 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: 661 Number of extensions: 31 Number of successful extensions: 1 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: 481 Length of database: 486 Length adjustment: 34 Effective length of query: 447 Effective length of database: 452 Effective search space: 202044 Effective search space used: 202044 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