Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_001046645.1:WP_066609128.1 Length = 487 Score = 565 bits (1456), Expect = e-165 Identities = 282/474 (59%), Positives = 356/474 (75%), Gaps = 2/474 (0%) Query: 3 LKDTQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP 62 L + LF ++AFI GAWV A +G T+ V+NPATG I+GTVP G A+T AI AA+ A P Sbjct: 5 LDNPALFIERAFIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFP 64 Query: 63 AWRALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEE 122 AW+A TA +RA L RW+ L++ N DL R+MT EQGKP+AEA+GEI YAASFI+WFAEE Sbjct: 65 AWKAQTAGDRAAVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEE 124 Query: 123 AKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 +R+ G ++P + ++R++V+K+P+GV+AAITPWNFPAAMITRK PALAAGC +V+KP+ Sbjct: 125 GRRVDGGIVPAPEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPS 184 Query: 183 SQTPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM 242 TPF+A ALA+LA+ AGIPAGVF++V+G IG LT++P+VRKLSFTGST +G LM Sbjct: 185 ELTPFTALALAKLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSLLM 244 Query: 243 SECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVY 302 +CA IK+VS ELGGNAP IVFDDAD+D AV A++SK+RN GQTCVCANR+ +QDGVY Sbjct: 245 RQCADTIKRVSFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVY 304 Query: 303 DAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVL--AGGKP 360 D FAEKL AV+ LK+ G G+T GPLI+ AV KVQ H+ DALS GAT+ A Sbjct: 305 DQFAEKLARAVSALKVAPGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAANDA 364 Query: 361 MEGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420 F P ILT + +A+EETFGP+APLFRF E + I ++N T +GLA+YFY + Sbjct: 365 TGARFATPVILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTEN 424 Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 L R FRVAE LE GMV +N+G I+ EVAPFGG+K SGLGREG+ GIE+YLE K Sbjct: 425 LHRAFRVAERLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETK 478 Lambda K H 0.317 0.135 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: 645 Number of extensions: 21 Number of successful extensions: 2 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: 480 Length of database: 487 Length adjustment: 34 Effective length of query: 446 Effective length of database: 453 Effective search space: 202038 Effective search space used: 202038 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 24 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