Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate PP_3180 PP_3180 Smp-30/Cgr1 family protein
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Putida:PP_3180 Length = 346 Score = 134 bits (336), Expect = 4e-36 Identities = 95/283 (33%), Positives = 142/283 (50%), Gaps = 12/283 (4%) Query: 14 GESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRGGWIAGMENG 73 GES VW R LY+VDI G ++ + +++ + +A RG I + Sbjct: 72 GESLVWDERSGVLYFVDISGGRINGLTPDGEVDCLYESAARIGALALTDRGNLIFTEDAS 131 Query: 74 LYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMAAGAVVGALYR 133 + +S ASV H ++ RFNDG CD QGRF G LMD A GAL+R Sbjct: 132 VAIFDV--PTRKVSQHSASV-HPRSTYRFNDGACDPQGRFVTG--LMDEALSDNTGALFR 186 Query: 134 YSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTDSGTPHDRRLF 193 + Q + + D+ +P GLA+S DG T+Y DS A + I+ +Y + G LF Sbjct: 187 FD-WQLSDQVIHDDMGLPTGLAWSHDGHTVYFVDS--AARAIYRAEYLIE-GRLGAVTLF 242 Query: 194 VDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKKPAMCAFGGPN 253 + LGRPDG A+D +G W+C + R+ +G L +++PV P C FGGP Sbjct: 243 AETPAELGRPDGLALDREGGLWVCQYHGSCLLRYDRHGYLTDQVLMPVPCPTSCCFGGPG 302 Query: 254 LDTLFVTSIR---PGGDLSDQPLAGGVFALRPGVKGLEEPVFQ 293 ++TL++++ R DL P AG ++A+RP G+ F+ Sbjct: 303 MNTLYISTARYDMTPEDLHHYPDAGDLYAIRPETGGVARHSFK 345 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: 366 Number of extensions: 20 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: 294 Length of database: 346 Length adjustment: 28 Effective length of query: 266 Effective length of database: 318 Effective search space: 84588 Effective search space used: 84588 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