Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD
Query= reanno::MR1:200453 (482 letters) >FitnessBrowser__Phaeo:GFF2918 Length = 491 Score = 617 bits (1592), Expect = 0.0 Identities = 311/482 (64%), Positives = 376/482 (78%), Gaps = 2/482 (0%) Query: 2 LLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAAL 61 LL DPSLL + YI G + D + T A+ NPA G VIA V + +++ AIA AE A Sbjct: 11 LLTDPSLLEPRAYIGGAFVDG-ADGTFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQ 69 Query: 62 PAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAE 121 W T KER LR+WF+L+ EN +DLA+++T+E GKPL E++GE+ Y ASFIE+FAE Sbjct: 70 KDWAKWTGKERANVLRKWFDLMMENQEDLAVILTAEMGKPLAESRGEIGYGASFIEFFAE 129 Query: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181 EAKRIYG+TIPGHQ DKRI V+KQP+GV A+ITPWNFP AMITRKA PALAAGC V +P Sbjct: 130 EAKRIYGETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARP 189 Query: 182 APQTPFTALALAVLAERAGIPAGVFSVITG-DAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240 A TP +A ALAVLA+RAGIPAGVF+V+T +A G E C N VRKL+FTGST VG Sbjct: 190 AELTPLSATALAVLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRI 249 Query: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300 LM Q A T+ K S+ELGGNAPFIVFDDA++DAAVEGA++ K+RN GQTCVCANRIYVQAG Sbjct: 250 LMRQAADTVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAG 309 Query: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360 VYD FA KL AVAK+ VG+G+ G GPLIN AVEKVQ+H+ DA +KGA V+ GG Sbjct: 310 VYDAFAAKLKEAVAKMTVGDGLAEGTQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNP 369 Query: 361 HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG 420 ELGG FFEPT++T A + M +++ETFGP+APLFKF DDVI+ ANDT FGLA+YFY Sbjct: 370 SELGGTFFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYA 429 Query: 421 RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480 +D+S V+KVAE+LEYG+VGVNTG+ISTE+APFGG+K SGLGREGS +GIE+YLE+KYICM Sbjct: 430 KDLSRVYKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYICM 489 Query: 481 SV 482 SV Sbjct: 490 SV 491 Lambda K H 0.318 0.133 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: 674 Number of extensions: 19 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: 482 Length of database: 491 Length adjustment: 34 Effective length of query: 448 Effective length of database: 457 Effective search space: 204736 Effective search space used: 204736 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