Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate BPHYT_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__BFirm:BPHYT_RS19720 Length = 515 Score = 407 bits (1045), Expect = e-118 Identities = 219/515 (42%), Positives = 330/515 (64%), Gaps = 4/515 (0%) Query: 1 MFASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMG 60 M +S T S P A+ EPYL + ++ FPGV+AL V L VR G V LMG Sbjct: 1 MTSSHTESHAAQAAPSP-ALASTEPYL-RLDGITVRFPGVLALDQVSLEVRRGEVHGLMG 58 Query: 61 ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA 120 ENGAGKSTL+K+++G+ QP AG L L G F T AA+ AG+A+I+QEL+L+P +++A Sbjct: 59 ENGAGKSTLLKVLSGVNQPAAGTLSLDGVEQQFITTKAAIAAGVAIIYQELHLVPELTVA 118 Query: 121 ENIWIGREQLNGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVS 180 EN+ +G N F ++D + + + LERL +DP +QV NLSI +RQM+EI KA+ Sbjct: 119 ENLMLGALP-NRFGILDEKALVARAVRELERLGEKIDPSQQVKNLSIGQRQMIEIGKALM 177 Query: 181 YDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDG 240 D+ ++ DEPTS+++ +E LF II LKA+G+ IIY+TH+M+EV+ + D V VFRDG Sbjct: 178 RDARVIAFDEPTSSLSSRETTQLFRIIRALKAEGRAIIYVTHRMDEVYELCDRVTVFRDG 237 Query: 241 AYIG-LQRADSMDGDSLISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDL 299 I + + +D D LIS MVGR ++ ++ R + +GD+ + V+++ G+ + SF Sbjct: 238 RRIDTFEAGEGLDRDRLISCMVGRSIADVYGYRSRDLGDVQLDVKEMMGRGLREPASFTA 297 Query: 300 HAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTED 359 GEI+G GL+G+GR+ + + I+G D GEI L G+ VR + P A+ G AL ED Sbjct: 298 RKGEIVGFFGLVGAGRSELMKLIYGAVKPDAGEIALKGKRVRFATPRDAVRAGVALCPED 357 Query: 360 RKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTL 419 RK G+ SV +N+ ++ H++ + + ++ KL +KT + + I TL Sbjct: 358 RKQEGIVSIASVSDNLNISCRRHFSRFNVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTL 417 Query: 420 SGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELP 479 SGGNQQK +L+RWL + + ++DEPTRGIDVGA++EIY L+ LA G VI++SS+L Sbjct: 418 SGGNQQKVILSRWLAEDIDVFLMDEPTRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLA 477 Query: 480 EVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLA 514 EV+G++DRV+VM EG ++G L +++AT + +++LA Sbjct: 478 EVIGVADRVIVMKEGRIVGDLPKAQATPDALIKLA 512 Score = 109 bits (272), Expect = 3e-28 Identities = 64/218 (29%), Positives = 121/218 (55%), Gaps = 5/218 (2%) Query: 51 RPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQE 110 R G ++ G GAG+S LMK+I G +PDAGE+ L+GK V F TP A++AG+A+ ++ Sbjct: 298 RKGEIVGFFGLVGAGRSELMKLIYGAVKPDAGEIALKGKRVRFATPRDAVRAGVALCPED 357 Query: 111 LN---LMPHMSIAENIWIG-REQLNGFHMIDHREMHRCTAQLLERLRINL-DPEEQVGNL 165 ++ S+++N+ I R + F++++ R+ + + + +L I + + +G L Sbjct: 358 RKQEGIVSIASVSDNLNISCRRHFSRFNVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTL 417 Query: 166 SIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMN 225 S +Q V +++ ++ D D+ +MDEPT I + ++ ++ L G+ +I ++ + Sbjct: 418 SGGNQQKVILSRWLAEDIDVFLMDEPTRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLA 477 Query: 226 EVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR 263 EV +AD V V ++G +G D+LI + + R Sbjct: 478 EVIGVADRVIVMKEGRIVGDLPKAQATPDALIKLALPR 515 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: 650 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: 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