Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BPHYT_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS19720 Length = 515 Score = 544 bits (1401), Expect = e-159 Identities = 279/493 (56%), Positives = 373/493 (75%), Gaps = 4/493 (0%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 LR D I FPGV ALD VS +V G+VHGLMGENGAGKSTLLK+L G QP +G + +D Sbjct: 26 LRLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLSLD 85 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKRE-AKRFVRE 123 G E +F + ++IAAG+A+I+QEL VP+LTVAENL+LG LPN G ++++ R VRE Sbjct: 86 GVEQQFITTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPNRFGILDEKALVARAVRE 145 Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183 LE +G +DP+ +++ LSI QRQM+EI KAL+R+ARVIA DEPTSSLS RET LF+++ Sbjct: 146 -LERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFRII 204 Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243 R L+A+ RA+IY++HRMDE+YELCD T+FRDGR+I + EG+ RD ++S MVGR I+ Sbjct: 205 RALKAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFEAGEGLDRDRLISCMVGRSIA 264 Query: 244 DIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGAD 303 D+Y Y +R LG+V+ K + G L +PASF R+GEIVGFFGLVGAGRSELM L+YGA Sbjct: 265 DVYGYRSRDLGDVQLDVKEMMGRGLREPASFTARKGEIVGFFGLVGAGRSELMKLIYGAV 324 Query: 304 HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRV 363 GE+ L GK ++ + +A+R G+ LCPEDRK+EGIV++A+VS+N+NISCRRH+ R Sbjct: 325 KPDAGEIALKGKRVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCRRHFSRF 384 Query: 364 GMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDE 423 + L+ +KEA+TA FI L IKT + I LSGGNQQK ILSRWLAE D+ V ++DE Sbjct: 385 NV-LNGRKEAQTAKEFIGKLAIKTRNGDTPIGTLSGGNQQKVILSRWLAE-DIDVFLMDE 442 Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483 PTRGIDVGA+ EIY ++Y LAE G ++++SS+L EV+GV+DR++VM++GRI G+L + Sbjct: 443 PTRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGDLPKAQ 502 Query: 484 ATEQSVLSLALPQ 496 AT +++ LALP+ Sbjct: 503 ATPDALIKLALPR 515 Lambda K H 0.320 0.136 0.385 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: 774 Number of extensions: 34 Number of successful extensions: 7 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: 512 Length of database: 515 Length adjustment: 35 Effective length of query: 477 Effective length of database: 480 Effective search space: 228960 Effective search space used: 228960 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 (21.8 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