Align succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)
to candidate BPHYT_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-20455 (480 letters) >FitnessBrowser__BFirm:BPHYT_RS34305 Length = 479 Score = 612 bits (1578), Expect = e-180 Identities = 298/468 (63%), Positives = 365/468 (77%), Gaps = 2/468 (0%) Query: 12 YINGEWLSALGGETQSIFNPATGQLIGTVPMMGRQEARQAIAAANQALPAWRALPAKERS 71 +I GEW G +T ++ NPATG+++ V G E QAIAAA +A PAWRAL AKERS Sbjct: 10 FIGGEWYE--GADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRALTAKERS 67 Query: 72 ARLRAWFELMLEHQEELARLMTIEQGKPLAEARNEILYAASFVEWFAEEGKRVYGDVIPS 131 AR++ W ELMLE+++ LA L+T+EQGKPLAEAR E+ YAASF EWFAEE KR YGDVIPS Sbjct: 68 ARVKRWGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPS 127 Query: 132 PQADKRLLVIKQPVGVTAAITPWNFPSAMITRKAAPALAAGCTMVLKPAPQTPFSALALA 191 P + +++V ++PVGV AAITPWNFP AMITRKA PALAAGCTMVLKP+ +TP SA ALA Sbjct: 128 PNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSAFALA 187 Query: 192 ALAQRAGIPAGVFNVVTGSAQEIGGEFTGNPIVRKLTFTGSTHIGRLLMAQCAHDVKKMS 251 LA +AGIP GVFN+V+G A IGG T + +VRKL+FTGST +G+LL Q A +KK+S Sbjct: 188 VLAAKAGIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLS 247 Query: 252 LELGGNAPFIVFEDADLDKAAEGALIAKYRNNGQTCVCTNRIYVHDSVHDAFAGKLKKAV 311 LELGGNAPFIVF+DADLD A +GA+ +K+RN GQTCVC NR YV D ++DAF L +AV Sbjct: 248 LELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTSALTQAV 307 Query: 312 EGLRVGNGLEDGVTVGPLINDAAVQKVRSHIADAVGKGASILAGGKPHALGGTFFEPTIL 371 +RVGN L+ V GPLIN AA++KV +H+ADA+ KGA IL GGKPH LGGTF+EPT+L Sbjct: 308 RKMRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGTFYEPTVL 367 Query: 372 ANVPHDALVAHEETFGPLAPLFRFRDEAEVVGRANDTEYGLAAYFYTENLGRIFRVAEAL 431 A+ + L+A EETFGP+A FRF+ EAE + ANDT +GL+AYFYT +L R +RV EAL Sbjct: 368 ADADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLARAWRVGEAL 427 Query: 432 EYGMVGINCGAISNEVAPFGGVKASGLGREGSKYGIEEYLEIKYLSLG 479 E GMVGIN G +S EVAPFGGVK SGLGREGSKYG++EY E+KY+ +G Sbjct: 428 ESGMVGINEGIVSTEVAPFGGVKQSGLGREGSKYGLDEYTELKYMMMG 475 Lambda K H 0.319 0.135 0.399 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: 701 Number of extensions: 20 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: 480 Length of database: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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