Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 5209155 Shew_1633 lipoprotein releasing system, ATP-binding protein (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__PV4:5209155 Length = 233 Score = 129 bits (324), Expect = 5e-35 Identities = 82/222 (36%), Positives = 128/222 (57%), Gaps = 17/222 (7%) Query: 4 LEVQDLHKRY--GS--HEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 L+V ++ KRY GS +VL GV+L A G+ ++IIGSSGSGKST L + L++P +G+ Sbjct: 10 LQVSNVSKRYHEGSIDTQVLSGVNLSIAKGEQVAIIGSSGSGKSTLLHIMGTLDKPSSGQ 69 Query: 60 ILLNNEEL-KLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHV 118 ++ + E+L +L ++ A++ L ++Q +L TA+EN+ P + Sbjct: 70 VMFDGEDLYQLSPSRQAAIR----------NQELGFIYQFHHLLPEFTALENVA-MPGLI 118 Query: 119 LGMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 + E ++A+ L++VG+ HR P MSGGE+QR AIARAL P+++L DEPT Sbjct: 119 QKRPRQEVEQEAKELLSRVGLGHRLHHTPAEMSGGERQRTAIARALINRPKLVLADEPTG 178 Query: 179 ALDPELVGDVLKVMQAL-AQEGRTMVVVTHEMGFAREVSNQL 219 LD V ++++ L +Q G VVVTH+ A + QL Sbjct: 179 NLDAASGDSVYELIRELGSQLGTAFVVVTHDPKLAARMDRQL 220 Lambda K H 0.317 0.131 0.366 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: 131 Number of extensions: 11 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: 254 Length of database: 233 Length adjustment: 23 Effective length of query: 231 Effective length of database: 210 Effective search space: 48510 Effective search space used: 48510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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