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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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