Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate AZOBR_RS31880 AZOBR_RS31880 sugar ABC transporter ATP-binding protein
Query= SwissProt::P37388 (513 letters) >FitnessBrowser__azobra:AZOBR_RS31880 Length = 515 Score = 277 bits (709), Expect = 6e-79 Identities = 174/502 (34%), Positives = 271/502 (53%), Gaps = 17/502 (3%) Query: 2 PYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEG 61 P +L + ITK FG + A D++ L L+ GE+++L GENG+GK+TLM +L G Y + EG Sbjct: 5 PIVLRLSGITKRFGPLVANDSISLTLHKGEVLALLGENGAGKTTLMNILFGHYV--ADEG 62 Query: 62 EIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTL 121 I G+ + R GI ++HQ L L+VL+NI +G E D Sbjct: 63 SIEAFGQPLPPGSPRAALAAGIGMVHQHFTLADNLSVLDNIAVGTESLWRPRSDRAAAKA 122 Query: 122 RCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSIL 181 + L + L + PD VGDL +G++Q EI KAL + R+LILDEPTA LT QE++ L Sbjct: 123 KLLDLARRFGLEVRPDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQESASL 182 Query: 182 LDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGR 241 D +R L G+A ++ISHK+NEV A SDT+ V+R G+ + TR A +++ +MVGR Sbjct: 183 FDTLRRLTADGLAVVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAELMVGR 242 Query: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301 L P P G+ +L + +T R + ++ V +++R +I+GIAG+ G G+T Sbjct: 243 ALKPPTPT-PLEPGEPVLTLSGVTVASGHGRPL--LDGVDLTVRRRQIVGIAGVSGNGQT 299 Query: 302 ETIQCLFG-VWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360 + + G + P G + + G+ + + + +G+A +PEDR G+V MAV +N Sbjct: 300 ALAELISGLIHPD--SGTMTLKGEAIGNAEPAEMVRRGVARIPEDRHAAGLVGAMAVWEN 357 Query: 361 ITL-----AALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAI 415 + A +F + A + E I V+ PD LSGGN QK I Sbjct: 358 LIAERYHDPAFQRF----GLIRRGAARAYAEEVIAAFDVRCPGPDARTQLLSGGNMQKLI 413 Query: 416 LARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRV 475 L R L P +++ +PTRG+D+GA ++ + + G V+VIS +L E+L L+D + Sbjct: 414 LGRTLAHGPDLILASQPTRGLDVGAVSYVHGRLLEARAAGAGVLVISEDLDEILALADGI 473 Query: 476 LVMHEGKLKANLINHNLTQEQV 497 V + G+L L + ++ Q+ Sbjct: 474 TVAYHGRLTPVLPHGRVSVRQL 495 Score = 88.2 bits (217), Expect = 6e-22 Identities = 64/222 (28%), Positives = 114/222 (51%), Gaps = 8/222 (3%) Query: 278 NDVSFSLKRGEILGIAGLVGAGRTETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQ 337 + +S +L +GE+L + G GAG+T + LFG + EG I G+ + + + A+A Sbjct: 24 DSISLTLHKGEVLALLGENGAGKTTLMNILFGHYVAD-EGSIEAFGQPLPPGSPRAALAA 82 Query: 338 GIAMVPEDRKRDGIVPVMAVGKNITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTS 397 GI MV + + ++V NI + + + + D AA + +L+ ++ ++ Sbjct: 83 GIGMV---HQHFTLADNLSVLDNIAVGTESLWR---PRSDRAAAKAKLLDLARRFGLEVR 136 Query: 398 SPDLAIGRLSGGNQQKAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIA 457 PD +G LS G +Q+A + + L + R+LILDEPT + ++ + +L G+A Sbjct: 137 -PDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQESASLFDTLRRLTADGLA 195 Query: 458 VIVISSELPEVLGLSDRVLVMHEGKLKANLINHNLTQEQVME 499 V+ IS ++ EV SD V V+ G+L A +E++ E Sbjct: 196 VVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAE 237 Lambda K H 0.319 0.137 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: 609 Number of extensions: 27 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: 513 Length of database: 515 Length adjustment: 35 Effective length of query: 478 Effective length of database: 480 Effective search space: 229440 Effective search space used: 229440 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