Align ABC transporter (characterized, see rationale)
to candidate BWI76_RS17830 BWI76_RS17830 ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Koxy:BWI76_RS17830 Length = 364 Score = 313 bits (803), Expect = 4e-90 Identities = 170/349 (48%), Positives = 228/349 (65%), Gaps = 4/349 (1%) Query: 6 LDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGR 65 L++V K G +++DVSL I GEF V VGPSGCGKSTLLR+IAGL+ I GG++ I+ R Sbjct: 6 LNSVRKSYGDAHVIKDVSLTIPDGEFCVLVGPSGCGKSTLLRMIAGLEEISGGEVHINER 65 Query: 66 RVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDK 125 V ++EP+ R + MVFQSYALYP M+V +N+ F LK+AK K + ++V + A +L L+ Sbjct: 66 NVTEVEPKLRDIAMVFQSYALYPQMTVRENMGFALKMAKLPKAEINQKVNEAAALLGLEP 125 Query: 126 LLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGS 185 LL+R PK+LSGGQRQRVAMGRA+ R+P + LFDEPLSNLDA LR Q+R EI LH RL + Sbjct: 126 LLERLPKDLSGGQRQRVAMGRAIVRKPQVFLFDEPLSNLDAKLRTQVRGEIRELHRRLKT 185 Query: 186 TMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSAR 245 T +YVTHDQ+EAMT+ IVVL GR+EQ G+P ELY+RPA+ FVAGF+GSP +N L Sbjct: 186 TSVYVTHDQIEAMTMGQMIVVLRDGRIEQAGTPLELYDRPANLFVAGFIGSPEINQLPGE 245 Query: 246 LQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSL--KAADGTAGVVVTAV 303 + G + + + +LP + G + IRPE V++ +A D VTAV Sbjct: 246 VVLNGNATSLRLKDGSLLALP-AGLRVTDGQQVVYAIRPEQVNVVHEARDDALAAKVTAV 304 Query: 304 EYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDA 352 E GS+ + +TG + + GD++ L L +HLFDA Sbjct: 305 ENTGSDMQLFCDTG-GGAFTSVFKQRLAVKEGDKIWLQPKLSGVHLFDA 352 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: 363 Number of extensions: 16 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: 381 Length of database: 364 Length adjustment: 30 Effective length of query: 351 Effective length of database: 334 Effective search space: 117234 Effective search space used: 117234 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