Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 16017 b1900 fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Keio:16017 Length = 504 Score = 373 bits (958), Expect = e-108 Identities = 224/489 (45%), Positives = 301/489 (61%), Gaps = 17/489 (3%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P L+ R I KTFPGV+AL + YAG+VHALMGENGAGKSTL+KILSG Y A G Sbjct: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNY-APTTGSV 64 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 I+GQ + +A + GVA+IYQEL L P ++VAENIYLG+ + G+V R + Sbjct: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 L LG D P + LSI Q Q+VEIA+A+ A+I+ DEPT+ LS E D LF Sbjct: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL-DRAHLSQAALVKMMVGRD 250 +IR+LR EG ILY+SHRM EI L+D +TV +DG +V T D + ALV+ MVGRD Sbjct: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244 Query: 251 LS---GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307 + G+ +++G+ ER + +V+ A G R S +R+GE++GL GLVGAGR+EL Sbjct: 245 IGDIYGWQPRSYGE--ERLRLDAVK--APGVRTP-ISLAVRSGEIVGLFGLVGAGRSELM 299 Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367 + +FG T G+V I + P AI AG+ EDRK +G+ SV Sbjct: 300 KGMFGGTQITAGQVYIDQQ-------PIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVR 352 Query: 368 ENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427 +NIN+ + LG +N I +L I+ A+ + LSGGNQQK +L R Sbjct: 353 DNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGR 412 Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487 L + +V++LDEPTRG+D+GAK EIY +I ALA GVA+L SS+LPEV+G+ DR++VM Sbjct: 413 WLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVM 472 Query: 488 REGTLAGEV 496 REG +AGE+ Sbjct: 473 REGEIAGEL 481 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: 606 Number of extensions: 27 Number of successful extensions: 8 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: 504 Length adjustment: 35 Effective length of query: 505 Effective length of database: 469 Effective search space: 236845 Effective search space used: 236845 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