Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__psRCH2:GFF4209 Length = 383 Score = 108 bits (270), Expect = 2e-28 Identities = 75/236 (31%), Positives = 129/236 (54%), Gaps = 16/236 (6%) Query: 3 QEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62 ++ +L + K++ A+D ++ GEI A++G +G+GKS++++ ++G P EG Sbjct: 19 KQVLLKIDRVTKKFDETVAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGR 78 Query: 63 IRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLD 122 I L+G+ I P E I ++Q+ AL P +++ N+ G +++ G L Sbjct: 79 IFLDGQDITDMPPYE---RPINMMFQSYALFPHMTVEQNIAFG--LKQDG--------LP 125 Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182 +A +E++ + L L MT Q + LSGGQRQ VA+AR+ A K++++DEP AL Sbjct: 126 KAEIEERVKEMLG-LVQMT-QYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 183 Query: 183 GVK-ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKD 237 K S+ LEL+ + R G+ V+++H+ +A+RI I LG V +P D Sbjct: 184 DKKLRSQMQLELVQIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMD 239 Lambda K H 0.321 0.136 0.383 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: 164 Number of extensions: 3 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: 260 Length of database: 383 Length adjustment: 27 Effective length of query: 233 Effective length of database: 356 Effective search space: 82948 Effective search space used: 82948 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: 48 (23.1 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