Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_044621444.1 H744_RS06405 ribose ABC transporter ATP-binding protein RbsA
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_000940995.1:WP_044621444.1 Length = 501 Score = 382 bits (981), Expect = e-110 Identities = 213/500 (42%), Positives = 321/500 (64%), Gaps = 4/500 (0%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 P L + I K FPGVKAL S + Y G+V ALMGENGAGKSTL+K L+G Y G + Sbjct: 4 PILELKDIEKAFPGVKALDKASLNVYPGKVMALMGENGAGKSTLMKALTGIYHMDAGEIR 63 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYEA 124 GQ ++F+ + AG++II+QEL+L+PE+T+AENI+LG + + G + S + EA Sbjct: 64 YQGQTVNFNGPRHSQEAGISIIHQELNLIPELTIAENIFLGREKTNAFGGIKWSQMYKEA 123 Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184 L L + T L LS+G+ QMVEIAKAL+ +++I DEPT +L+ E ++LF+ Sbjct: 124 DALLARLNVKHSSRTLLGDLSLGEQQMVEIAKALSFKSQVIIMDEPTDALTDTETESLFK 183 Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244 VI ELR+EG I+Y+SHR++EIF + D ITV +DG+++ + +D D +++ MVGR Sbjct: 184 VINELREEGTGIVYISHRLKEIFEICDDITVLRDGKFIGQRA-VADIDEDTMIEMMVGRR 242 Query: 245 IGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304 + + Y +G L + + PGV +S + GEI+G+ GL+GAGR+ELMK ++G Sbjct: 243 LDEQYPRIDVKHGTTCLAVKNLNGPGVHD-VSFTLDRGEILGISGLMGAGRTELMKVIYG 301 Query: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364 + +G V +D + I+ P +A G+ EDRK +G+I SV++N++I + + + Sbjct: 302 ALERESGDVVLDGKVINPLTPQDGLANGIAYISEDRKGDGLILGLSVKENMSICSLEQ-L 360 Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424 G + + E + IR NIKTP Q+I NLSGGNQQK + + L + KV++LD Sbjct: 361 SKGIQLRHYDEVTAVEDFIRLFNIKTPTHNQIIGNLSGGNQQKVAIAKGLMTKPKVLILD 420 Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484 EPTRG+DVGAK EIY +I ++G++++ SS++PEVLG++DRI+VM EG+I+GE + E Sbjct: 421 EPTRGVDVGAKKEIYQLINQFKSEGMSIILVSSEMPEVLGMSDRILVMHEGKISGEFMAE 480 Query: 485 QADERQALSLAMPKVSQAVA 504 +AD+ + L+ A+ K VA Sbjct: 481 EADQEKLLACAVGKQINEVA 500 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: 706 Number of extensions: 36 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 24 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