Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__BFirm:BPHYT_RS19720 Length = 515 Score = 405 bits (1042), Expect = e-117 Identities = 220/495 (44%), Positives = 317/495 (64%), Gaps = 8/495 (1%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64 P L++ GI F LAL + L +R GE+H LMGENGAGKSTL+KVLSGV+ P G + Sbjct: 24 PYLRLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLS 83 Query: 65 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124 LDG A+ AAG+ +IYQEL + P ++VA N+ +G+ L R G++D A+ +R Sbjct: 84 LDGVEQQFITTKAAIAAGVAIIYQELHLVPELTVAENLMLGA-LPNRFGILDEKALVARA 142 Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 L +LG S LSI ++Q +EI +AL+ +R++ DEPT++LS RET QLF Sbjct: 143 VRELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFR 202 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDE-IDSERIVQMMVGRS 243 ++R L+ EG AIIY++HRM EVY L DRVTV RDG + E +D +R++ MVGRS Sbjct: 203 IIRALKAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFEAGEGLDRDRLISCMVGRS 262 Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIR-PASFDVRAGEVLGFAGLVGAGRTELA 302 +++ Y ++ D + V+ + G +R PASF R GE++GF GLVGAGR+EL Sbjct: 263 IADVYGYRSRDLGDVQ-----LDVKEMMGRGLREPASFTARKGEIVGFFGLVGAGRSELM 317 Query: 303 RLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362 +L++GA G+I L+G+ V PR A+RAG+A PEDRK +G+ +V+ N ++ Sbjct: 318 KLIYGAVKPDAGEIALKGKRVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISC 377 Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422 +R ++ R A+ I +L +K + +TP+G LSGGNQQKV+L+RWL V Sbjct: 378 RRHFSRFNVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTLSGGNQQKVILSRWLAEDIDV 437 Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482 ++DEPTRG+D+ A+SEIY L++ LA G V+V+SS+L EVIG+ DRV+VM+EG I G+ Sbjct: 438 FLMDEPTRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGD 497 Query: 483 LAGAAITQENIMRLA 497 L A T + +++LA Sbjct: 498 LPKAQATPDALIKLA 512 Score = 92.4 bits (228), Expect = 3e-23 Identities = 66/232 (28%), Positives = 112/232 (48%), Gaps = 29/232 (12%) Query: 28 TIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIY 87 T R GEI G GAG+S LMK++ G PD GEI L G+ V P + AG+ L Sbjct: 296 TARKGEIVGFFGLVGAGRSELMKLIYGAVKPDAGEIALKGKRVRFATPRDAVRAGVALCP 355 Query: 88 QE---------LAVAPNISVAA-------NVFMG-SELRTRLGLIDHAAMRSRTDAVLRQ 130 ++ +V+ N++++ NV G E +T I A+++R Sbjct: 356 EDRKQEGIVSIASVSDNLNISCRRHFSRFNVLNGRKEAQTAKEFIGKLAIKTRN------ 409 Query: 131 LGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLR 190 G LS QQ+V ++R L + +MDEPT + +++ ++ L Sbjct: 410 ------GDTPIGTLSGGNQQKVILSRWLAEDIDVFLMDEPTRGIDVGARSEIYGLLYGLA 463 Query: 191 DEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 + G +I +S +AEV +ADRV V+++G VG+L + + + ++++ + R Sbjct: 464 EAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGDLPKAQATPDALIKLALPR 515 Lambda K H 0.320 0.135 0.378 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: 733 Number of extensions: 35 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: 521 Length of database: 515 Length adjustment: 35 Effective length of query: 486 Effective length of database: 480 Effective search space: 233280 Effective search space used: 233280 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