Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate SMa0717 SMa0717 hypothetical protein
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Smeli:SMa0717 Length = 569 Score = 191 bits (484), Expect = 4e-53 Identities = 111/295 (37%), Positives = 161/295 (54%), Gaps = 13/295 (4%) Query: 2 DAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAAD 61 D + ++ GE+PVW RE+ LYWVDI + +HR+D + S ++++ + Sbjct: 282 DVQCVLPWGAQLGEAPVWVEREKRLYWVDILHPAVHRFDPVTGKNESCNVAKLVSAVLPT 341 Query: 62 SRGGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMD 121 G I ++G+ H D G A E R ND + D GR W G+M +D Sbjct: 342 RNEGLIVASQDGVEHFD-FDRGDF--NPFAEPEPGLPENRLNDAKVDPSGRLWVGSMRLD 398 Query: 122 MAAGAVVGALYRY-SAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDY 180 ++ G+LYR SAG+ T V NGLA+SPD T Y D+ P + I+A+D+ Sbjct: 399 VSRPT--GSLYRLTSAGEVTRAGS--GFTVANGLAWSPDSSTFYFVDTVPGI--IYAYDF 452 Query: 181 DTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVP 240 D G+ +RR+FV + GRPDG A+DADG W D V+R+ P+G+LDR++ +P Sbjct: 453 DAREGSIANRRVFVTVPEAEGRPDGLAVDADGGVWCAIWDGWRVNRYRPDGRLDRAVELP 512 Query: 241 VKKPAMCAFGGPNLDTLFVTSIR---PGGDLSDQPLAGGVFALRPGVKGLEEPVF 292 V +P AFGG L TLF+TS R P L++ PL+GG+FA PG +GL +F Sbjct: 513 VPRPTSVAFGGDELATLFITSARTRLPASTLTEAPLSGGIFACNPGARGLPTSLF 567 Lambda K H 0.320 0.138 0.441 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: 582 Number of extensions: 39 Number of successful extensions: 5 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: 294 Length of database: 569 Length adjustment: 31 Effective length of query: 263 Effective length of database: 538 Effective search space: 141494 Effective search space used: 141494 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: 50 (23.9 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