Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate 7024914 Shewana3_2088 hypothetical protein (RefSeq)
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__ANA3:7024914 Length = 300 Score = 140 bits (354), Expect = 3e-38 Identities = 97/295 (32%), Positives = 146/295 (49%), Gaps = 12/295 (4%) Query: 5 LIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRG 64 + + N GE +W Q+++W DI + ++R+ + ++ P + ++ Sbjct: 11 MTIPVGNRLGEGVLWDDLHQSIWWTDILSSVIYRFHLASRSLETFPMPHRVGSFGLTAKP 70 Query: 65 GW-IAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMA 123 I + G+ + +D SL T LA E G RFNDGR DRQGRFWAGTM+ Sbjct: 71 TTLIVAFDIGIA-IYDIEDQSL--TWLAQPESHFAGNRFNDGRIDRQGRFWAGTMVEQRD 127 Query: 124 AGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTD 183 ALY + L +L + NGL +S DG+T+Y +DS +I+ +D+D + Sbjct: 128 TLQQTAALYCLDE-KGHCHQHLTNLEISNGLCWSVDGRTLYHADSPK--HQIYQYDFDIE 184 Query: 184 SGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKK 243 G +RLF ++++ PDG+ +DA G W G V R+ P+G++D L +PV Sbjct: 185 QGLLSRKRLFASTSHHIF-PDGSDVDAAGYLWNAQWGGGQVVRYRPDGEVDLILKLPVTH 243 Query: 244 PAMCAFGGPNLDTLFVTSIRPGGD---LSDQPLAGGVFAL-RPGVKGLEEPVFQG 294 P AFGG D L VTS + D L +P AG VF G+ G+ P F G Sbjct: 244 PTSIAFGGEKRDLLIVTSAKHSLDASQLDQEPQAGDVFIYPLQGIYGVNSPRFCG 298 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: 292 Number of extensions: 23 Number of successful extensions: 6 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: 300 Length adjustment: 26 Effective length of query: 268 Effective length of database: 274 Effective search space: 73432 Effective search space used: 73432 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: 48 (23.1 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