Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_012969141.1 KVAR_RS23745 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_000025465.1:WP_012969141.1 Length = 506 Score = 389 bits (999), Expect = e-112 Identities = 212/495 (42%), Positives = 312/495 (63%), Gaps = 7/495 (1%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 +TP L R I K F AL + + G++HALMGENGAGKSTL+KIL+G Y T+G Sbjct: 3 ATPVLEMRHIAKAFGKFYALKGVDLTVWPGEIHALMGENGAGKSTLMKILAGAYTATSGE 62 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123 ++I+G+ + AL AG+ +IYQE+ L P +TVAENI+LG +GG+V R + + Sbjct: 63 ILIDGKPQTIRGPKDALAAGITLIYQEMQLAPNLTVAENIFLGSELARGGLVQRKAMLSQ 122 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A + LG + L+I + Q VEIA+AL R ++I+ DEPT++LS+RE LF Sbjct: 123 AQAVIDRLGAQFKASDRVMTLTIAEQQQVEIARALHRQSRILVMDEPTAALSSRETQRLF 182 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 +I LR EG I+Y+SHRM E++ LSD ++V +DG+YV + +++ LV+ MVGR Sbjct: 183 ELILRLRDEGMAIIYISHRMAEVYELSDRVSVLRDGQYVGSLV-RDKLNAPELVRMMVGR 241 Query: 244 DIGDIYGWQ---PRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300 + D++ + PR G+ RLR++ + G P SL V +GEIVGL GLVGAGRSEL + Sbjct: 242 PLSDLFNKERDIPR--GQPRLRVEDLTDGGKVKPSSLVVHAGEIVGLAGLVGAGRSELAQ 299 Query: 301 GMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360 +FG + T G + ID +P+ I P AI G+ E+RK +G+ + ++NI ++ Sbjct: 300 LIFGVRKATGGVIEIDGEPVVIHSPREAIDLGIGFLTENRKEQGLFLELAAQENITMATL 359 Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420 + G ++N + +D I+ LNI+ P A+ LSGGNQQK ++ RW++ ++ Sbjct: 360 ERDANWG-MLNRRKAQTISDDAIQLLNIRVPHAQVRAGGLSGGNQQKLLISRWVAIGPRI 418 Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480 ++LDEPTRG+DVGAK EIY ++ +A QGVA+L SS+LPEV+G++DR+ VMREG IAGE Sbjct: 419 LILDEPTRGVDVGAKSEIYRIMNDMARQGVAILMISSELPEVVGMSDRVYVMREGAIAGE 478 Query: 481 LLHEQADERQALSLA 495 L + ++LA Sbjct: 479 LQAGDISQENIMTLA 493 Lambda K H 0.319 0.136 0.391 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: 655 Number of extensions: 28 Number of successful extensions: 7 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: 504 Length of database: 506 Length adjustment: 34 Effective length of query: 470 Effective length of database: 472 Effective search space: 221840 Effective search space used: 221840 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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