Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 392 bits (1007), Expect = e-113 Identities = 226/508 (44%), Positives = 318/508 (62%), Gaps = 11/508 (2%) Query: 24 EPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA-- 81 E L E+ ++K F GV AL + LR+R G L L GENGAGKSTLMK+++G+Y + Sbjct: 4 ESCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWD 63 Query: 82 GELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREM 141 GE+ +G+P+ + + +AGI +IHQEL L+P +S+AENI++G E +D+ M Sbjct: 64 GEILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAM 123 Query: 142 HRCTAQLLERLRIN-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEV 200 + LL+ L ++ ++ + +Q+ EIAKA++ + +LI+DEPTS++T E Sbjct: 124 YAKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSET 183 Query: 201 AHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMM 260 L I+ DLK +G IYI+HK++EV + D V V RDG +I Q +D D+LI++M Sbjct: 184 EVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLM 243 Query: 261 VGRELSQLFPVREKPIGDLLMSVRDLR-LDGV------FKGVSFDLHAGEILGIAGLMGS 313 VGR+L L+P E IG+++ R LD V VSF L GEILGIAGL+G+ Sbjct: 244 VGRKLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGA 303 Query: 314 GRTNVAEAIFGI-TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVL 372 GRT + AIFG T E+ L+G+P++I P AI G ++ EDRK G+ P L V Sbjct: 304 GRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVG 363 Query: 373 ENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARW 432 +N+ +A L HYA G I ++ E + RVKT S I LSGGNQQKA+LA+ Sbjct: 364 DNITLATLDHYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKM 423 Query: 433 LMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMH 492 L+ P++LILDEPTRG+DVGAKAEIYRLI LA++G+A++++SSE+PEVLGM+DRV+VM Sbjct: 424 LLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMG 483 Query: 493 EGDLMGTLDRSEATQERVMQLASGMSVR 520 EG L G TQE+V+ A S R Sbjct: 484 EGRLRGDFPNQGLTQEQVLAAAIDTSAR 511 Score = 80.5 bits (197), Expect = 1e-19 Identities = 63/230 (27%), Positives = 109/230 (47%), Gaps = 6/230 (2%) Query: 294 GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITP--SDGGEICLDGQPVRISDPHMAIEK 351 G+ L AGE LG+ G G+G++ + + + G+ P S GEI GQP+R + Sbjct: 25 GIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEILWQGQPLRARSVRDSERA 84 Query: 352 GFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPS 411 G ++ ++ L P LSV EN+ + G G + A+ A + + ++L + + Sbjct: 85 GIVIIHQELML---VPQLSVAENIFLGHEITRPG-GRMDYDAMYAKADALLQELGLHDVN 140 Query: 412 LEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAV 471 + GG+QQ +A+ L ++LILDEPT + + ++ L G+A Sbjct: 141 VALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVLLGIVEDLKRRGVAC 200 Query: 472 IMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSVRH 521 I IS +L EV + D V V+ +G + T E + ++ L G + + Sbjct: 201 IYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGRKLEN 250 Lambda K H 0.321 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: 692 Number of extensions: 38 Number of successful extensions: 10 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: 513 Length adjustment: 35 Effective length of query: 486 Effective length of database: 478 Effective search space: 232308 Effective search space used: 232308 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