Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_084931762.1 HA51_RS02835 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_002095475.1:WP_084931762.1 Length = 500 Score = 164 bits (415), Expect = 3e-45 Identities = 95/248 (38%), Positives = 146/248 (58%), Gaps = 13/248 (5%) Query: 7 LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66 L RG+ K YG AL DF + PGE+ A+IG+NGAGKS+++ +SG D G I + Sbjct: 6 LMMRGITKTYGSAIALQDVDFMVRPGEVHALIGENGAGKSTLLNILSGVRPADSGAIHVN 65 Query: 67 GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126 G+ +Q ++P+ AR AGI ++Q L P LS+A NMFLGR + +L+ + Sbjct: 66 GEQVQMKNPLSARHAGIAMIHQELQHVPELSVAQNMFLGRPL----------TTLNGLFV 115 Query: 127 EKQAR-AKLSELGLMTIQNINQA--VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183 +K+A+ A+ + + +IN A ++ L Q+Q V +ARA +K++ MDEPT++L Sbjct: 116 DKRAQLARATHILKQLDPSINPAEPIKNLKVSQQQIVEIARALLDEAKIIAMDEPTSSLT 175 Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDA 243 +E R+ ELI D++ G+ ++ +SH M +F+V DR I R GR++ V+N D T Sbjct: 176 PREFERLAELIADLKSTGVSLIYVSHKMNEIFQVCDRATIMRDGRQVGVVNICDETEETI 235 Query: 244 VAFMTGAK 251 VA M G K Sbjct: 236 VAKMVGRK 243 Score = 93.6 bits (231), Expect = 7e-24 Identities = 69/239 (28%), Positives = 116/239 (48%), Gaps = 13/239 (5%) Query: 13 VKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQF 72 V+ R T + A F + GE+L V G GAG++ ++K I+G GE+R+ G+ ++ Sbjct: 261 VENVARGTEIKPASFSVCAGEVLGVAGLVGAGRTELLKLIAGIDKRSAGEVRVNGQLVRN 320 Query: 73 RSPMEARQAGIETVYQNL---ALSPALSIADNMFLG--REIRKPGIMGKWFRSLDRAAME 127 + A +AGI V ++ + A ++ NM L R G++ K L+ A E Sbjct: 321 HNVSAAIRAGIGLVPEDRKKEGIIKARAVKVNMALPSMRNFTLAGVIRKV--KLNAVAQE 378 Query: 128 KQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKES 187 + KL L NI + + TLSGG +Q V + R A ++V + DEPT + + Sbjct: 379 VMSDLKLRPL------NIEKPIGTLSGGNQQKVIIGRWVAADAEVFLFDEPTRGIDIGAK 432 Query: 188 RRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAF 246 + LI + ++G IV++S M + V+DR+ + R G+ + D T + F Sbjct: 433 AEIYNLIEKLAQQGKAIVVVSSEMTEILRVSDRVLVMREGKITRELTGDDITEENIARF 491 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: 283 Number of extensions: 14 Number of successful extensions: 4 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: 500 Length adjustment: 29 Effective length of query: 231 Effective length of database: 471 Effective search space: 108801 Effective search space used: 108801 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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