Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 386 bits (992), Expect = e-112 Identities = 213/503 (42%), Positives = 312/503 (62%), Gaps = 6/503 (1%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64 PLL +RG+ K+F AL + T+R GEIHAL+GENGAGKSTL+K L+GV+ D G + Sbjct: 11 PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVT 70 Query: 65 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124 L+GR +A R ++ I +YQE+ + PN+SVA N+F+G + R GL+D AMR R Sbjct: 71 LEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQ-PMRFGLVDRGAMRRRA 129 Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 AVL G + GR S+A QQ V IARA+ ++++I+DEPTA+L +E LF Sbjct: 130 RAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFK 189 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 V+R LR G+ I++++H + +VYAL DR+TVLR+G VGE E+ +V MM+GR L Sbjct: 190 VMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGREL 249 Query: 245 SEFYQHQRIAPADAAQ---LPTVMQVRALAGGK-IRPASFDVRAGEVLGFAGLVGAGRTE 300 E H+ PAD A+ P +++ R + + P D+R GEV+G AGL+G+GRTE Sbjct: 250 -EAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTE 308 Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360 ARL+FG D G+ ++G+ V + PR A+R G + PEDRK +G+ ++V N + Sbjct: 309 TARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIIL 368 Query: 361 NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420 + +R L + +A I+ L+++ H E P+ LSGGNQQK LLARWL P Sbjct: 369 ALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEP 428 Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480 ++LILDEPTRG+D+ A +EI +L+ RL + G+A++V+SSEL E++ RV+V+R+ Sbjct: 429 RLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHV 488 Query: 481 GELAGAAITQENIMRLATDTNVP 503 EL G + + I+ +VP Sbjct: 489 AELRGGEVAVDRIVAAIASESVP 511 Score = 98.6 bits (244), Expect = 5e-25 Identities = 71/247 (28%), Positives = 118/247 (47%), Gaps = 9/247 (3%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64 PL++ RG +G ++ L IRPGE+ L G G+G++ +++ G+ D+GE Sbjct: 270 PLVRFRG----YGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAA 325 Query: 65 LDGRPVALRDPGASRAAGINLIYQEL---AVAPNISVAANVFMGSELRTR-LGLIDHAAM 120 +DG+ V LR P + G ++ + +SV N+ + + R L I Sbjct: 326 VDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLRPIPRCRQ 385 Query: 121 RSRTDAVLRQLGAGFG-ASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 179 D +R L A LS QQ+ +AR L R++I+DEPT + Sbjct: 386 EEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAH 445 Query: 180 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMM 239 ++ ++ RL +G+A++ +S + E+ A + RV VLRD V EL E+ +RIV + Sbjct: 446 AEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAAI 505 Query: 240 VGRSLSE 246 S+ E Sbjct: 506 ASESVPE 512 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: 732 Number of extensions: 30 Number of successful extensions: 8 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: 516 Length adjustment: 35 Effective length of query: 486 Effective length of database: 481 Effective search space: 233766 Effective search space used: 233766 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