Align Phosphoserine phosphatase RsbP; EC 3.1.3.3 (uncharacterized)
to candidate WP_078429615.1 BK574_RS18670 PAS domain S-box protein
Query= curated2:O07014 (403 letters) >NCBI__GCF_002019605.1:WP_078429615.1 Length = 404 Score = 477 bits (1227), Expect = e-139 Identities = 227/404 (56%), Positives = 311/404 (76%), Gaps = 1/404 (0%) Query: 1 MDKQLNDAPCGFLALSEEGSIIAANRTLIKILDYEPEQVIGQHMNMMLTIPAQLFCQLYF 60 MD+QLN APCGF+ L+EEG+II N++L+++L Y +++ QH++ +LT PAQ+F QLYF Sbjct: 1 MDEQLNYAPCGFVTLTEEGTIITINQSLLRLLGYREDELDQQHIHKILTAPAQMFYQLYF 60 Query: 61 FPLLKLEHHIEEIYISLKARDGEEIPVLINAIARHDSGASVFDCVLIPMRKRNEYENELL 120 FPL+K+E +EE+Y+SL+ + GEEIP+L+NA +V DCV IP+RKR+EYENELL Sbjct: 61 FPLVKIEGKVEEMYLSLRMKTGEEIPILLNAKQNQRENITVIDCVFIPVRKRDEYENELL 120 Query: 121 IARNEAQEALLAKQKANAELEIALETLKAKQEELLEINKQNQQFKLNTKRELELARKIQK 180 IA+ EA+ AL AK + NAELEIAL+TL+ KQ EL+++NK+NQ++KL+T ++LELARKIQ+ Sbjct: 121 IAKKEAEAALHAKNQTNAELEIALQTLETKQVELVQLNKENQKYKLDTSKKLELARKIQE 180 Query: 181 NSLTEPIVNDQVQIDSYYNASSELSGDLYGYYQIDEHRYGIIILDVMGHGISSALITMSL 240 SLT+PI N+ ++I +YY ASS+LSGD+YG+YQI HRYG++ILDVMGHGISSALITMSL Sbjct: 181 TSLTDPIDNEHIEIQAYYKASSQLSGDIYGFYQIGSHRYGVMILDVMGHGISSALITMSL 240 Query: 241 HPLFQRQITQGLSPVKVMKELDRHLHSLFQNDEEARHYCTAIYLEIDIARQRIDYVNAGH 300 LFQR I++G +P VM ELD +LHSLF N+EE RHYCTA Y +D +++I+Y+NAGH Sbjct: 241 QSLFQRLISRGFTPEHVMSELDHYLHSLFHNNEETRHYCTAFYAVVDTYKEQIEYINAGH 300 Query: 301 PPALWQDDSGTQHLLHATSPPIGMFEDLEFQSSSLSYTEDGRLLLYTDGVMDP-TASCYL 359 PP L Q +G L ATSPP+G+ + FQS +L Y + +LLLYTDGV DP L Sbjct: 301 PPTLLQHANGEVDELSATSPPVGLLNGIRFQSKTLPYAKGSKLLLYTDGVEDPIEEDSRL 360 Query: 360 FDLLKDHPDSPIADLKEKILTSLQHQKEAHHKSDDECFILVDVK 403 +L + D P++ LKEK++ + H+ A+HK+DD+CFILV++K Sbjct: 361 RAILASNLDVPLSTLKEKLIAGISHEANAYHKNDDQCFILVNLK 404 Lambda K H 0.319 0.136 0.388 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: 524 Number of extensions: 26 Number of successful extensions: 2 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: 403 Length of database: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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