Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Length = 526 Score = 427 bits (1099), Expect = e-124 Identities = 224/494 (45%), Positives = 325/494 (65%), Gaps = 6/494 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL++ + K F +ALSD+ L +RPG + ALMGENGAGKSTLMK+++G++ PD GE+ L Sbjct: 32 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G+PV P A+ AGI +I+QEL + P++S+A N+++G E L +IDH M T Sbjct: 92 RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 +L +L +L G LSIAE+Q VEIA+A+ + S I+IMDEPT+A++++E LF++ Sbjct: 152 KLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 211 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245 + L+ +G IIYI+H+M EV+++AD V V RDG+++G D +D + ++ MMVGR LS Sbjct: 212 IADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 271 Query: 246 EFYQHQRIAPADAAQLPTVMQVRAL-AGGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304 + + + D ++ VR L G + SFD+ AGE+LG AGL+G+GRT +A Sbjct: 272 QLFPVREKPIGD-----LLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEA 326 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364 +FG P GG+I L+G V I P A+ G A + EDRK GLF ++V N M V Sbjct: 327 IFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 386 Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424 + G ++ ++L + ++L VK E + LSGGNQQK LLARWL P++LI Sbjct: 387 HYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILI 446 Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484 LDEPTRG+D+ AK+EIY+L+ LAS+G+AV++ISSELPEV+G+ DRV+VM EG + G L Sbjct: 447 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLD 506 Query: 485 GAAITQENIMRLAT 498 + TQE +M+LA+ Sbjct: 507 RSEATQERVMQLAS 520 Score = 103 bits (256), Expect = 2e-26 Identities = 67/225 (29%), Positives = 116/225 (51%), Gaps = 5/225 (2%) Query: 24 DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83 D+ + GEI + G G+G++ + + + G+ D GEI LDG V + DP + G Sbjct: 299 DVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGF 358 Query: 84 NLIYQELAVA---PNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASD 139 L+ ++ ++ P +SV N+ M G I A+R+ + + ++L + + Sbjct: 359 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLE 418 Query: 140 LA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 198 LS QQ+ +AR L+ RI+I+DEPT + +++ ++ L EG+A+I Sbjct: 419 QCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIM 478 Query: 199 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243 IS + EV ++DRV V+ +G +G L R E ER++Q+ G S Sbjct: 479 ISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 523 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: 665 Number of extensions: 25 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 526 Length adjustment: 35 Effective length of query: 486 Effective length of database: 491 Effective search space: 238626 Effective search space used: 238626 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