Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 142 bits (357), Expect = 2e-38 Identities = 85/245 (34%), Positives = 141/245 (57%), Gaps = 10/245 (4%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L + K + V ALD+ D + GE+ A++G+NGAGKS++IK +S A D G + Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 66 EGKPIQFR-SPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 G+ + R +P+ +Q GI T+YQ L P LS+A+NM+LGRE R+ G++ D + Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLV-------DWS 115 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 + A+A L++LGL N + V L+ ++Q V +A+A ++++IMDEPTAAL Sbjct: 116 RLRADAQALLNDLGLPL--NPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSG 173 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 +E R+ +I ++ R + ++ +SH + V + DR + R GR + + D ++D V Sbjct: 174 REVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMV 233 Query: 245 AFMTG 249 M G Sbjct: 234 RLMVG 238 Score = 93.6 bits (231), Expect = 8e-24 Identities = 70/248 (28%), Positives = 122/248 (49%), Gaps = 11/248 (4%) Query: 6 ILTARGLVKRYGRVTA---LDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62 +L G+ R++A L + F GEI+ + G GAG++ + + I GA G Sbjct: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315 Query: 63 IRLEGKPIQFRSPMEARQAGIETVYQNLALSPAL---SIADNMFLGREIRKPGIMGKWFR 119 + ++ KP++ RSP +A QAGI V ++ SI N+ L ++ +G+W Sbjct: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP-SLKALSALGQWVD 374 Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 + + R KL + + + A+ LSGG +Q V + RA A KV+I+DEPT Sbjct: 375 ERAERDLVETYRQKLR----IKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPT 430 Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239 + + V +++ D+ G+ +V+IS + V V+DRI + R G + ++ + T Sbjct: 431 RGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTAT 490 Query: 240 MSDAVAFM 247 +A+M Sbjct: 491 EEGLMAYM 498 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: 324 Number of extensions: 17 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: 515 Length adjustment: 29 Effective length of query: 231 Effective length of database: 486 Effective search space: 112266 Effective search space used: 112266 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