Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 6937316 Sama_1486 ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__SB2B:6937316 Length = 249 Score = 135 bits (339), Expect = 1e-36 Identities = 94/248 (37%), Positives = 135/248 (54%), Gaps = 17/248 (6%) Query: 1 MYKLEVQDLHKRYGSHE----VLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPH 56 M+ ++V L K+ + E +LKGV ++ G+ ++IIG SGSGKST L + L+ P Sbjct: 4 MHAIKVVHLKKKVQTQEGELTILKGVDMEVKPGESVAIIGPSGSGKSTLLGLLAALDTPS 63 Query: 57 AGKILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPV 116 G+I L+ L +N KAA K+ ++S +FQ F L +TA+EN+M P Sbjct: 64 EGEIWLDGSAL---SNLGEEAKAALRKK------KISFIFQSFMLVDTLTALENVM-LPA 113 Query: 117 HVLGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEP 176 + GM A+A KAE L +VG+SHR + P +SGGEQQRVAIARA EP+V+ DEP Sbjct: 114 ELAGMKDAKA--KAEAMLERVGLSHRVNHLPKQLSGGEQQRVAIARAFICEPKVLFADEP 171 Query: 177 TSALDPELVGDVLKVMQAL-AQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPRE 235 T LD V ++ AL A+ G T+V+VTH+ A Q + E + Sbjct: 172 TGNLDGGNAHKVADMLFALNAELGTTLVLVTHDNQLALRCQRQFTMTEGELAETTAAQEA 231 Query: 236 VLVNPQSE 243 + Q+E Sbjct: 232 PRQDAQAE 239 Lambda K H 0.317 0.131 0.364 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: 155 Number of extensions: 10 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: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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