Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__HerbieS:HSERO_RS05320 Length = 502 Score = 368 bits (945), Expect = e-106 Identities = 225/506 (44%), Positives = 298/506 (58%), Gaps = 13/506 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 +L L I K F V LR V+L AGEVHAL+GENGAGKSTLMKIL G D GE Sbjct: 1 MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPD-AGEIR 59 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 131 IDGQ + D ++A GV V++QE SL P L +N++L R L+ R G + R M R Sbjct: 60 IDGQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRRRA 119 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 + +LG V LS+AQ+Q VEIA+A+ +ARILV+DEPT L+ E + LFA Sbjct: 120 QEIIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFA 179 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 ++R LR +G+AI++ISH + EI E+ DR+TVLRDG +V T A + QA LV+MMVGR + Sbjct: 180 VMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGRRI 239 Query: 252 SGFYTK--THGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309 + G E EV+L V + R+ F LR GE+LG AGLVG+GRTE Sbjct: 240 ENCFPPKPAKGGEGEGEVVLEVHALQLRRQAPVSQFQLRRGEILGFAGLVGSGRTETVLA 299 Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369 + GA A ++ + V L P QA+ AGI L E RK QGL S+ N Sbjct: 300 MLGAHAALSCKLSMHG-------VPLRFADPAQALQAGIGLLPESRKEQGLITSFSILHN 352 Query: 370 INLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 429 ++L + LG L+R ++ T A+ + ++ AQV V LSGGNQQKV+++R + Sbjct: 353 VSLNNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIARWI 412 Query: 430 EIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMRE 489 +VLI DEPTRG+D+GAKSEIY+L+ G +ILMISSELPEVVG+ DRV V R Sbjct: 413 NHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVFRG 472 Query: 490 GTLAGEVRPAGSAAETQERIIALATG 515 G + + G A +E + TG Sbjct: 473 GGIVATLE--GEAVNAEEIMTHATTG 496 Lambda K H 0.320 0.136 0.382 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: 643 Number of extensions: 29 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 540 Length of database: 502 Length adjustment: 35 Effective length of query: 505 Effective length of database: 467 Effective search space: 235835 Effective search space used: 235835 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: 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