Align ABC transporter (characterized, see rationale)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 241 bits (614), Expect = 3e-68 Identities = 146/338 (43%), Positives = 209/338 (61%), Gaps = 13/338 (3%) Query: 15 GMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLD-SICGGDLLIDGRRVNDLEPR 73 G L+ + L+I AGE VV +GPSGCGK+T LR+IAGL+ GG ++ V L Sbjct: 19 GTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGDNDVTPLPIE 78 Query: 74 ERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKE 133 +RGVGMVFQSYAL+P+M+V +NI++GL++ + D + R RV + ++ L +R+ + Sbjct: 79 QRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRIDQ 138 Query: 134 LSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHD 193 LSGGQRQRVA+ RA+A +P +LL DEPL+ LDA LR +R +I +L L T +YVTHD Sbjct: 139 LSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSLHITAVYVTHD 198 Query: 194 QVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETS 253 Q EAM L D+I+V++ GR+ Q G+P+++Y PA+ FVA F+G+ MN L A L+ Sbjct: 199 QAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNRLPAVLEADAW-- 254 Query: 254 LVDTLVWGITSLPFDSSNLAAGTP--LSLGIRPEHVSLKAADGT--AGVVVTAVEYLGSE 309 + G+ +++LAA L RPE V+L A+ G VVTA+ +LG+ Sbjct: 255 ---RVPGGLVPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTAL-FLGNY 310 Query: 310 TYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNL 347 T + ++ G PL+ GW AGDRV L LD +L Sbjct: 311 TRLLVDVGAPAPLVVDTTRRDGWLAGDRVGLRLDTGHL 348 Lambda K H 0.320 0.137 0.394 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: 321 Number of extensions: 14 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: 381 Length of database: 357 Length adjustment: 30 Effective length of query: 351 Effective length of database: 327 Effective search space: 114777 Effective search space used: 114777 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: 49 (23.5 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