Align ABC transporter (characterized, see rationale)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Keio:14980 Length = 377 Score = 229 bits (583), Expect = 1e-64 Identities = 129/323 (39%), Positives = 195/323 (60%), Gaps = 10/323 (3%) Query: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63 L++ N+ K G + DVSL I GE +G SGCGKSTLLR++AG + G +++D Sbjct: 20 LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79 Query: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123 G ++ + P R + M+FQSYAL+PHM+V NI+FGLK K K + RV + ++ + Sbjct: 80 GVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHM 139 Query: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183 + +RKP +LSGGQRQRVA+ R++A+ P +LL DEP+ LD LR +M+ E+ + +R+ Sbjct: 140 QEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERV 199 Query: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLS 243 G T + VTHDQ EAMT+A +I ++N G+ Q+G P E+YE P +R+ A F+GS +N Sbjct: 200 GVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS--VNVFE 257 Query: 244 ARLQTPGETSLVDTLVWGITSLPFDS-SNLAAGTPLSLGIRPEHVSL---KAADGTAGVV 299 L+ E LV + L D+ +++ P+ + +RPE + L A+G V Sbjct: 258 GVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAV 317 Query: 300 --VTAVEYLG--SETYVHLETGQ 318 V + YLG S +V L++GQ Sbjct: 318 GEVIHIAYLGDLSVYHVRLKSGQ 340 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: 349 Number of extensions: 19 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 351 Effective length of database: 347 Effective search space: 121797 Effective search space used: 121797 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