Align ABC transporter (characterized, see rationale)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 359 bits (921), Expect = e-104 Identities = 201/368 (54%), Positives = 247/368 (67%), Gaps = 13/368 (3%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M ++L NV K G + + +D++L+I GEFVVFVGPSGCGKSTLLR+IAGL++I GDL Sbjct: 1 MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 I +R+ND P ERGVGMVFQSYALYPH+SV +N+SFGLKLA K + +RV + A++ Sbjct: 61 FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 LQL LL RKPK LSGGQRQRVA+GR + EP + L DEPLSNLDA+LRVQMR EI+RLH Sbjct: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 RLG TMIYVTHDQVEAMTLADKIVVL+ GRV QVG P ELY PA RFVAGF+GSP+MN Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 Query: 241 FLSARLQTPGETSLVDTL-------VWGITSLPFDSSNLAAGTPLSLGIRPEH-VSLKAA 292 FL ++ + L VW LP +S ++ G +SLGIRPEH + A Sbjct: 241 FLPVKVTATAIDQVQVELPMPNRQQVW----LPVESRDVQVGANMSLGIRPEHLLPSDIA 296 Query: 293 DGTAGVVVTAVEYLGSETYVHLETGQ-DEPLICRCEVSAGWQAGDRVELLLDLDNLHLFD 351 D V VE LG+ET +H++ + L+ R + G + L + HLF Sbjct: 297 DVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFR 356 Query: 352 ADGVALSR 359 DG A R Sbjct: 357 EDGTACRR 364 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: 361 Number of extensions: 13 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: 371 Length adjustment: 30 Effective length of query: 351 Effective length of database: 341 Effective search space: 119691 Effective search space used: 119691 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