Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 372 bits (956), Expect = e-107 Identities = 203/493 (41%), Positives = 312/493 (63%), Gaps = 6/493 (1%) Query: 6 PYL-SFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 PYL I K FPGV AL D+ G V ALMGENGAGKSTL+KI++G Y P G + Sbjct: 21 PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEI 80 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG--QLPHKGGIVNRSLLNY 122 + G+ + F AA AG+A+I+QEL+L+P M++AENI++G QL + +R + Sbjct: 81 RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRC 140 Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 A L L L +++DP+ + LSI + QMVEIAKA++ ++ I+ DEPTS+++ +E+ +L Sbjct: 141 TAEL-LARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHL 199 Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242 F +I +L+ +G+ I+Y++H+M E+FA++D + VF+DG Y+ ++ D+L+ MVG Sbjct: 200 FSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVG 258 Query: 243 RDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 R++ ++ + G+ L + + GV +S + +GEI+G+ GL+G+GR+ + + + Sbjct: 259 RELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETI 318 Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362 FG T ++GQ+ +D + + I P AI G L EDRK G+ P SV +N+ ++ Sbjct: 319 FGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-P 377 Query: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422 H G I + + L +KTP EQ I LSGGNQQKA+L RWL ++++ Sbjct: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437 Query: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482 LDEPTRGIDVGAK EIY +I LA++G+AV+ SS+LPEVLG++DR++VM EGE+ G L Sbjct: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497 Query: 483 HEQADERQALSLA 495 +A + + + LA Sbjct: 498 RSEATQEKVMQLA 510 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: 616 Number of extensions: 27 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: 517 Length adjustment: 35 Effective length of query: 469 Effective length of database: 482 Effective search space: 226058 Effective search space used: 226058 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 Apr 09 2024. 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