Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 296 bits (758), Expect = 1e-84 Identities = 171/470 (36%), Positives = 257/470 (54%), Gaps = 4/470 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPD-GQAEDARKAIDAAERAQPEWEALPAIER 68 Y G + A V NPA VI+ +PD G+AE AR AI AA+ AQ W A A +R Sbjct: 23 YFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETAR-AIAAADAAQKPWAARTAKDR 81 Query: 69 ASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 A LR+ I A +++ ++ E GK A EV + A ++++ AE A+R GE I Sbjct: 82 AQVLRRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIP 141 Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188 P I + ++ +GV I PWNFP +I RK APAL G + KP+E TP +A+A Sbjct: 142 GHLPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALAL 201 Query: 189 AKIVDEIGLPRGVFN-LVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITK 247 A + + G+P G+F L +G+E N V ++ TGS G ++A AA + K Sbjct: 202 AVLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKK 261 Query: 248 VCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGE 307 +ELGG AP IV DDADL+ AV+ + + N+GQ C CA R+YVQ G+YD F +L Sbjct: 262 CSMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAA 321 Query: 308 AMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPP 367 A++ ++ G+ A + +GPLIN A+E+V+ + +G V GG+ G ++ P Sbjct: 322 AVEELKVGDGAAEG-VTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTP 380 Query: 368 TLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAI 427 T++ V QEM + EETFGPV P+ F ++ I+MAND+ +GL Y +++ + Sbjct: 381 TVVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVS 440 Query: 428 KGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 + L++G IN G ++SG+G +HG+ EYL+ + + L Sbjct: 441 EALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICL 490 Lambda K H 0.318 0.135 0.392 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: 550 Number of extensions: 25 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: 479 Length of database: 492 Length adjustment: 34 Effective length of query: 445 Effective length of database: 458 Effective search space: 203810 Effective search space used: 203810 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