Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_009543699.1 CCE_RS19935 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000017845.1:WP_009543699.1 Length = 455 Score = 192 bits (488), Expect = 2e-53 Identities = 144/468 (30%), Positives = 226/468 (48%), Gaps = 21/468 (4%) Query: 55 IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARARILLKAAAILKRR 114 I ++NP T E V T+ + E L A F ++K ++ R++ L AA IL+R Sbjct: 3 IATVNPA-TGETVKIFEPITVDEIEVKLALAETTFRQYRKISLEQRSQWLKAAADILERD 61 Query: 115 RLEACALMSIEVGKNYAEADVEVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGLMS 174 + + +M++E+GK A E + YYA +A ++ ++T + + + Sbjct: 62 QQKLGEIMTLEMGKPIKGAIAEAKKCALVCRYYADNAAEFLKDVEAQT---DASRSFIRY 118 Query: 175 IPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAG 234 PLGV +++ PWNFP AA ++AGN ++K A + A + IL EAG PAG Sbjct: 119 QPLGVILAVMPWNFPLWQVFRFAAPALMAGNVGILKHASNVPQCALAVEAILAEAGFPAG 178 Query: 235 VLQ-FLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELG 293 Q FL +G E + + + T TGS G + A K IK+ ++ELG Sbjct: 179 CFQTFL--IGASEVESIINDPRVKAATLTGSEPAGASLASAAGKQ------IKKTVLELG 230 Query: 294 GKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALK 353 G D IV E+ADIE A T A NGQ C A R I+ +S+ DE +E+ KALK Sbjct: 231 GSDPFIVLESADIEAAATTAVTARMLNNGQSCIAAKRFILAESIADEFQALLLEKFKALK 290 Query: 354 MGTG-EENANVTAVVNQMSFNKIKGYL-ELAPSEGKVLLGGEATGEANGKQGYYIQPTIV 411 +G EE+ ++ + N ++ + E G +LLGG + + GY+ PTI+ Sbjct: 291 VGDPMEEDTDIGPLANASMLLELNQQVQETVTKGGTILLGGHIISD---RPGYFYPPTIL 347 Query: 412 GDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEF 471 D+ +S +E FGPV + R KD A+++AN T +GL +N ++ + Sbjct: 348 TDIPVDSPGYYDEFFGPVALLFRVKDIDQAIELANDTIFGLGASAWTNDSAEQDRLIEDI 407 Query: 472 EVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519 E G ++ N + PFGG SG + + + F+ +KTV Sbjct: 408 EAGCVFINGMVKSD--PRLPFGGIKRSGYGREL-SIEGMQEFLNVKTV 452 Lambda K H 0.317 0.134 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: 502 Number of extensions: 18 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: 523 Length of database: 455 Length adjustment: 34 Effective length of query: 489 Effective length of database: 421 Effective search space: 205869 Effective search space used: 205869 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 (21.6 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