Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 236 bits (602), Expect = 1e-66 Identities = 163/486 (33%), Positives = 251/486 (51%), Gaps = 18/486 (3%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 T L GI K +PG A I G++HAL+GENGAGKSTL+KI+ G P G + Sbjct: 6 TARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEI 65 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124 G+ ++ D A G+ +++Q L ++VAENI L L K G + L + Sbjct: 66 HWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALA-LGAKAGTPKQ--LEPKI 122 Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184 + GM ++P + LSIG+ Q VEI + L ++ +++ DEPTS L+ +E D LF Sbjct: 123 REVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 182 Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244 +R L EG IL++SH++ E+ AL + TV + GR + D + L + MVG D Sbjct: 183 TLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLE-LARLMVG-D 240 Query: 245 IGDIYGWQPRSYGE------ERLRLDAVKAPGVR-TPISLAVRSGEIVGLFGLVGAGRSE 297 + P+S G ERL GV + L VR+GEIVG+ G+ G G+ E Sbjct: 241 AEGLEAEYPKSEGRAPFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQDE 300 Query: 298 LMKGMFGGTQITAGQV----YIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRD 353 L+ + G ++ A Q ++ +R P GM P +R G +P S+ D Sbjct: 301 LLALLSGEQRLQAAQAMRIRFLGDDVAHLR-PGARRRHGMAFVPAERLGHGAVPSMSLAD 359 Query: 354 NINISA-RRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGR 412 N ++A ++ ++ +I G A+ I+ +KTP A+ +LSGGN QK ILGR Sbjct: 360 NGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGR 419 Query: 413 WLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVM 472 + ++ K+++ PT G+DVGA I+ + L G A+L S DL E+ ++DRI + Sbjct: 420 EILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAAL 479 Query: 473 REGEIA 478 +G ++ Sbjct: 480 SDGRLS 485 Score = 83.2 bits (204), Expect = 2e-20 Identities = 59/224 (26%), Positives = 114/224 (50%), Gaps = 18/224 (8%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334 I L+++ GEI L G GAG+S LMK ++G TQ AG+++ + + +R P+ A G+ Sbjct: 27 IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGI- 85 Query: 335 LCPEDRKAEGIIPVH-SVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTP-- 391 G++ H S+ + ++++ LG + IR ++ + Sbjct: 86 ---------GMVFQHFSLFETLSVAENIALALGA----KAGTPKQLEPKIREVSQRYGMP 132 Query: 392 -GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGV 450 ++L+ +LS G +Q+ + R L +++++++LDEPT + E++ + LAA+G Sbjct: 133 LEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGC 192 Query: 451 AVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSL 494 ++LF S L EV + V+R G ++GE + + + + L Sbjct: 193 SILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARL 236 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: 593 Number of extensions: 27 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 504 Length of database: 518 Length adjustment: 35 Effective length of query: 469 Effective length of database: 483 Effective search space: 226527 Effective search space used: 226527 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