Align ABC transporter (characterized, see rationale)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Koxy:BWI76_RS01840 Length = 369 Score = 365 bits (938), Expect = e-106 Identities = 203/366 (55%), Positives = 249/366 (68%), Gaps = 11/366 (3%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M ++L NV K G + + +D++LEI GEFVVFVGPSGCGKSTLLR+IAGL+++ GDL Sbjct: 1 MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSGDL 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 LI R+ND+ P ERG+GMVFQSYALYPH+SV +N+SFGLKLA K + +RV + A++ Sbjct: 61 LIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVAEV 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 LQL LL+RKPK LSGGQRQRVA+GR + EP + L DEPLSNLDA+LRVQMR EI+RLH Sbjct: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 RLG TMIYVTHDQVEAMTLADKIVVL+ GRV QVG P ELY PA RFVAGF+GSP+MN Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 Query: 241 FLSARLQTPGETSLVDTL-----VWGITSLPFDSSNLAAGTPLSLGIRPEH-VSLKAADG 294 FL ++ + L VW LP DS+ + G +SLGIRPEH + AD Sbjct: 241 FLPVKVTATAIEQVQVELPNRQQVW----LPVDSARVQVGANMSLGIRPEHLLPSDIADV 296 Query: 295 TAGVVVTAVEYLGSETYVHLETGQ-DEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353 T V VE LG ET +H++ + L+ R + G + L + HLF D Sbjct: 297 TLEGEVQVVEQLGHETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFRED 356 Query: 354 GVALSR 359 G A R Sbjct: 357 GTACRR 362 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: 366 Number of extensions: 9 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: 369 Length adjustment: 30 Effective length of query: 351 Effective length of database: 339 Effective search space: 118989 Effective search space used: 118989 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: 50 (23.9 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