Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 365 bits (938), Expect = e-105 Identities = 199/500 (39%), Positives = 309/500 (61%), Gaps = 5/500 (1%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 S P ++ R + K FPGV AL + F+ AG+VHALMGENGAGKSTL+KILSG Y +G Sbjct: 19 SVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGD 78 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHK--GGIVNRSLLN 121 ++++G+ + ++ A G+ II+QEL+L+ ++ A+NI++G+ P K G ++ LN Sbjct: 79 ILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELN 138 Query: 122 YEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDN 181 +A + +D+DP TP+ L++ + QMVEIAKAL+ +++++ DEPT++L+ EI Sbjct: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198 Query: 182 LFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMV 241 LFR+IR+L+ +G I+Y+SH+M+E+ ++D ++V +DG+Y+ T MQ+ D ++ MV Sbjct: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIAT-VPMQETSMDTIISMMV 257 Query: 242 GRDIGDIYGWQP-RSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300 GR + P S + L + + +S +R GEI+G GL+GAGR+E+ + Sbjct: 258 GRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVAR 317 Query: 301 GMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360 +FG + AG++ I I+ P+ A+A G+ EDRK G+ V+ NI +S+ Sbjct: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377 Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420 + G + E A ++R L IKTP EQ LSGGNQQK ++ +WL + + Sbjct: 378 GRFTRVGFMDQRAIREA-AQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436 Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480 + DEPTRGIDVGAK EIY ++ ALA QG A++ SS+LPEVL ++ R++VM EG I GE Sbjct: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496 Query: 481 LLHEQADERQALSLAMPKVS 500 L A + + + LA + S Sbjct: 497 LARADATQEKIMQLATQRES 516 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: 688 Number of extensions: 33 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: 504 Length of database: 520 Length adjustment: 35 Effective length of query: 469 Effective length of database: 485 Effective search space: 227465 Effective search space used: 227465 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 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