Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 360 bits (923), Expect = e-104 Identities = 201/505 (39%), Positives = 319/505 (63%), Gaps = 12/505 (2%) Query: 1 MTDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60 MT+++P++ ++GI FPGV+ALDGV LT+ PGEVHALMGENGAGKST++K L G+++ + Sbjct: 1 MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD 60 Query: 61 AGSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKK 119 G I+V +P +G LDA+ GI ++QE++L LSV EN+ LG R FG +DW + Sbjct: 61 EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE 120 Query: 120 THEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANE 179 L ++ + + T + +SIA QQ+V IARA+ ++AK +I DEPT+SL E Sbjct: 121 LEAKTNAILEKLKV-GFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAE 179 Query: 180 VRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGM 239 LF ++ +++ GV I ++SH +++I++ITDR+++LR+GQ+ V T +T + + M Sbjct: 180 KVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQM 239 Query: 240 MIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLG 299 MIG+ +LS+ A E+ ++V+GL V+ ++ +GEVVGF GL+G Sbjct: 240 MIGRK-LDLSRNEAHHELGEVA------LEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVG 292 Query: 300 SGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVR 359 +GRTE+ L+G P SG+ L+G +V I+ P+ A++ I+ E+R+ +G++ + R Sbjct: 293 AGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCR 352 Query: 360 QNILIALQATRGMFKPIPKKEAD-AIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418 N+ + Q P A+ AI D+Y +L++R + V NLSGGNQQK++IG+ Sbjct: 353 DNMTLP-QVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGK 411 Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478 WL+ P +LI+DEPTRGID+G+KAEI ++ DLA+QG V+ ISSE+ EV+ ++D I V Sbjct: 412 WLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRI-VA 470 Query: 479 KDRHKIAEIENDDTVSQATIVETIA 503 +I + V++ ++ I+ Sbjct: 471 MYSGRIMRTFTSEEVTEENLIAAIS 495 Score = 76.3 bits (186), Expect = 2e-18 Identities = 54/230 (23%), Positives = 107/230 (46%), Gaps = 17/230 (7%) Query: 24 DGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAG 83 + V+ + GEV G GAG++ + + L G+ +GSI +DG DA G Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332 Query: 84 IATVYQE---VNLCTNLSVGENVMLGHE---KRGPFGIDWKKTHEAAKKYLAQMGLESID 137 I+ V ++ L ++ +N+ L K GPF D A+ + + +D Sbjct: 333 ISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVAD------GAEIAIFDQYRDKLD 386 Query: 138 PHTP-----LSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRD 192 TP + ++S QQ + I + + + VLI+DEPT +D ++ ++R + Sbjct: 387 IRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAA 446 Query: 193 SGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 G A++ +S + ++ + DR+ + +G+ ++ +++ + LI + G Sbjct: 447 QGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496 Lambda K H 0.316 0.135 0.376 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: 663 Number of extensions: 32 Number of successful extensions: 9 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: 513 Length of database: 503 Length adjustment: 34 Effective length of query: 479 Effective length of database: 469 Effective search space: 224651 Effective search space used: 224651 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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