Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_010960469.1 MCA_RS05815 sulfate/thiosulfate import ATP-binding protein CysA
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000008325.1:WP_010960469.1 Length = 348 Score = 143 bits (360), Expect = 5e-39 Identities = 89/251 (35%), Positives = 144/251 (57%), Gaps = 21/251 (8%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +E++++ K +GS + LKG+ L +G++++++G SG GK+T LR I LE +G+ILL+ Sbjct: 3 IEIRNITKSFGSFQALKGIDLTIGSGELVALLGPSGCGKTTLLRIIAGLEAADSGQILLH 62 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENI-MEAPVHVLGMS 122 E D R+ VFQH+ L+ HM+ ENI V G Sbjct: 63 GE---------------DTTHRHVRERRVGFVFQHYALFRHMSVFENIAFGLRVRPRGQR 107 Query: 123 KTEA--REKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180 EA R + + L V + D +PG +SGG++QR+A+ARALA+EP+V+L DEP AL Sbjct: 108 PPEAEIRRRVQELLELVQLDWLADRHPGQLSGGQRQRIALARALAVEPKVLLLDEPFGAL 167 Query: 181 DPELVGDVLKVMQALAQEGR--TMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLV 238 D ++ D+ + ++ L +G T V VTH+ A EV++++V L+ G +E+ G+ EV Sbjct: 168 DAKVRKDLRRWLRRL-HDGLHITSVFVTHDQEEALEVADRVVVLNAGQIEQVGSADEVYD 226 Query: 239 NPQSERLQQFL 249 +P + + QF+ Sbjct: 227 HPATPFVCQFI 237 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: 181 Number of extensions: 7 Number of successful extensions: 3 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: 348 Length adjustment: 26 Effective length of query: 228 Effective length of database: 322 Effective search space: 73416 Effective search space used: 73416 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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