Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Smeli:SMc02337 Length = 501 Score = 377 bits (969), Expect = e-109 Identities = 213/495 (43%), Positives = 308/495 (62%), Gaps = 6/495 (1%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 T +S GI K F GV+AL + FD AG+VHAL+GENGAGKSTL+++L+G PT+G+V Sbjct: 2 TVLVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTV 61 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124 I+G+ M S A G+++I+QEL L P++TVAENI+LG+LP IVN L A Sbjct: 62 SIHGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPR---IVNHRRLRKAA 118 Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184 L+ LG DIDP L++ Q+VEIAKAL+ A+II FDEPT+ L+ + + L Sbjct: 119 SEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLLA 178 Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244 +IRELR G +Y+SHR+ E+F LSD ITV KDG +V+T + D DA++ MVGR Sbjct: 179 IIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETL-ETSATDVDAVIARMVGRQ 237 Query: 245 IGDIYGWQP-RSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMF 303 + ++ + R GE +R+ V +S +VR+GE+VGL GLVG+GR+E+ + +F Sbjct: 238 MSALFPSKAGRVPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLVF 297 Query: 304 GGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKH 363 G ++ +G V ++ +P+ + P A+ A + L PEDRK +G+I +R N ++ R Sbjct: 298 GADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKIRSI 357 Query: 364 VLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILL 423 G ++ G E A + +K + + +LSGGNQQK L +W + +++L Sbjct: 358 SRLG-FLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHADCDLLIL 416 Query: 424 DEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLH 483 DEPTRG+DVGAK EIYN+I LA G A+L SS+ E+ G+ DR++VM EG I GEL Sbjct: 417 DEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGELTE 476 Query: 484 EQADERQALSLAMPK 498 + E+Q L+LAM + Sbjct: 477 SKFTEQQLLTLAMTR 491 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: 674 Number of extensions: 35 Number of successful extensions: 9 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: 501 Length adjustment: 34 Effective length of query: 470 Effective length of database: 467 Effective search space: 219490 Effective search space used: 219490 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