Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 397 bits (1019), Expect = e-115 Identities = 222/500 (44%), Positives = 327/500 (65%), Gaps = 14/500 (2%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTG-SV 64 P+L R I +TFPGVKAL ++ + AG+V AL GENGAGKSTL+KIL+G YAP G ++ Sbjct: 8 PFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTI 67 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPH-KGGIVNRSLLNYE 123 ++ GQE++ +D+ A GV IIYQEL +V +TV ENI+L + P + G+++R + E Sbjct: 68 LVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYRE 127 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A L + MDIDP T + LS+GQ QM+EIAKAL +K I DEPT+SLS E L Sbjct: 128 AREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLL 187 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 +++ LR+ ++Y+SHR+EEIF L+D +TV +DGR V T + + + LV+ MV R Sbjct: 188 GIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGT-APIADMTRETLVRLMVAR 246 Query: 244 DIGDIYGWQPRSYGEER--LRLDAVKAPGVRTP------ISLAVRSGEIVGLFGLVGAGR 295 ++ ++YG +P+S+ L + A+ VR IS + GE++G+ GLVG+GR Sbjct: 247 ELSELYG-EPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGR 305 Query: 296 SELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNI 355 +E+M+ +FG T G V I+ +P+ IR P AI +G+ EDRKA+G+I +VR+N Sbjct: 306 TEIMEMIFGMRACT-GSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENF 364 Query: 356 NISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLS 415 +++ ++ V + E + +R L IKTPG EQ ++NLSGGNQQK ++ +W++ Sbjct: 365 SLTHLERYSPFQFV-QHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVA 423 Query: 416 EEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREG 475 KV+++DEPTRGIDVGAK E++ +I LAA+G+ V+ SSDL EVL V+DRI+ +REG Sbjct: 424 RSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREG 483 Query: 476 EIAGELLHEQADERQALSLA 495 I+GEL QA + + ++LA Sbjct: 484 RISGELSRAQASQEKVMALA 503 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: 658 Number of extensions: 33 Number of successful extensions: 10 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: 505 Length adjustment: 34 Effective length of query: 470 Effective length of database: 471 Effective search space: 221370 Effective search space used: 221370 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