Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Marino:GFF2860 Length = 672 Score = 110 bits (276), Expect = 6e-29 Identities = 75/234 (32%), Positives = 120/234 (51%), Gaps = 11/234 (4%) Query: 10 RGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKP 69 RG+ + + ALD L GE+LA++G++G GK+++ + I G P G + L G+ Sbjct: 366 RGMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQAPSTGSVTLNGQR 425 Query: 70 IQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQ 129 I+ PM+ R I+ ++Q+ P S+ +G I KP + + + Q Sbjct: 426 IENLPPMD-RARMIQPIFQD----PYSSLNPRKTIGEIIAKP----LFVHGIGSNQEQHQ 476 Query: 130 ARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRR 189 K+ EL + + N + LSGGQRQ A+ RA +VVI DEPT+AL V + Sbjct: 477 QVRKMMELVGLPSRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQ 536 Query: 190 VLELILDVR-RRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242 +L L+LD+R L + ++HN+ V +ADR+ + LG + +D MSD Sbjct: 537 ILNLLLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLG-EIVECGERDQVMSD 589 Score = 68.2 bits (165), Expect = 4e-16 Identities = 57/210 (27%), Positives = 100/210 (47%), Gaps = 17/210 (8%) Query: 28 DLYPGEILAVIGDNGAGKSSMIKAISGAVTP----DEGEIRLEGKPIQFRSPME----AR 79 +L GE L ++G++G+GKS A+ + P I +G + + E R Sbjct: 32 ELNRGETLGIVGESGSGKSMTALALMNLLPPAAKRQASCIDFDGSDLTHATERELASKIR 91 Query: 80 QAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGL 139 I ++Q P S+ +GR++++ + R + E +A L ++GL Sbjct: 92 GQRIGMIFQ----EPMTSLNPVYSIGRQLKETMTL---HRKVSDTEAENRAVYLLEKVGL 144 Query: 140 M-TIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVR 198 + Q LSGGQRQ V +A A +++I DEPT AL V ++L L+ +++ Sbjct: 145 PDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLIADEPTTALDVTIQAQILHLLRELQ 204 Query: 199 RR-GLPIVLISHNMPHVFEVADRIHIHRLG 227 + G+ ++LI+H++ V AD I + G Sbjct: 205 QEFGMSMILITHDLGVVSRAADNIAVMYAG 234 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: 388 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 672 Length adjustment: 31 Effective length of query: 229 Effective length of database: 641 Effective search space: 146789 Effective search space used: 146789 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