Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 159 bits (403), Expect = 9e-44 Identities = 97/248 (39%), Positives = 145/248 (58%), Gaps = 9/248 (3%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 A P+L RGL K + V ALD DF + GEI A++G+NGAGKS++IK ++G D G Sbjct: 8 ASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAG 67 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121 + LEG+ I R EA++ I TVYQ + L P LS+A+N+FLGR+ + G+ + Sbjct: 68 TVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGL-------V 120 Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 DR AM ++ARA L GL ++ + S +Q VA+ARA +KV+I+DEPTA+ Sbjct: 121 DRGAMRRRARAVLIPYGLTL--DVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTAS 178 Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 L +E + +++ +R RG+ IV ++H + V+ + DRI + R GR + + Sbjct: 179 LDAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRL 238 Query: 242 DAVAFMTG 249 D VA M G Sbjct: 239 DLVAMMLG 246 Score = 92.4 bits (228), Expect = 2e-23 Identities = 61/255 (23%), Positives = 124/255 (48%), Gaps = 13/255 (5%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 A+ P++ RG YG+ +++ D D+ PGE++ + G G+G++ + + G D G Sbjct: 267 ARPPLVRFRG----YGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRG 322 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWF 118 E ++G+ ++ R P +A + G ++ + ALS+ +N+ L + R+ W Sbjct: 323 EAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQ-----GWL 377 Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEP 178 R + R E+ A + L + T + Q ++ LSGG +Q +AR A +++I+DEP Sbjct: 378 RPIPRCRQEEIADRFIRLLDIRT-PHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEP 436 Query: 179 TAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDY 238 T + V ++ LI + G+ ++++S + + + R+ + R R + + + Sbjct: 437 TRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEV 496 Query: 239 TMSDAVAFMTGAKEP 253 + VA + P Sbjct: 497 AVDRIVAAIASESVP 511 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: 334 Number of extensions: 21 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: 516 Length adjustment: 29 Effective length of query: 231 Effective length of database: 487 Effective search space: 112497 Effective search space used: 112497 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 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