Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__HerbieS:HSERO_RS22465 Length = 518 Score = 390 bits (1002), Expect = e-113 Identities = 220/500 (44%), Positives = 315/500 (63%), Gaps = 11/500 (2%) Query: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--GE 79 YLLE+ I K F GV AL + +++RPG + L GENGAGKSTLMKI++G+Y GE Sbjct: 4 YLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEGE 63 Query: 80 IRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHR 139 I GKP+ + + AGI +IHQEL L+P +S+AENI++G E +N+ M+R Sbjct: 64 ILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPAMYR 123 Query: 140 CTAELLARLRI-NLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198 EL+ L + +++ V +Q+VEIAKA++ D+ +LI+DEP+S++T E+ Sbjct: 124 RAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIGV 183 Query: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258 L II DLK++G VYI+HK++EV + D ++V RDG +I M+ D +I+ MVG Sbjct: 184 LLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMVG 243 Query: 259 RELSQLFPLRETPIGDLLLTVRDLTLDGV-------FKDVSFDLHAGEILGIAGLMGSGR 311 RE++ ++P R IG+++L R++T + DVSF + GEILGIAGL+G+GR Sbjct: 244 REITAMYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVGAGR 303 Query: 312 TNVAETIFGITPSS-SGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLEN 370 T + IFG GQ+ L+GK S P +I +G ++ EDRK G+ P L V +N Sbjct: 304 TELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPDLDVGQN 363 Query: 371 MEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 430 + + VL ++ I A +D ++RVKT + I +LSGGNQQKA+LA+ L+ Sbjct: 364 ITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAVLAKMLL 423 Query: 431 TNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEG 490 P++LILDEPTRG+DVGAKAEIYRLI+ LA G+A+IM+SSEL EVLG+SDRV+V+ EG Sbjct: 424 AQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRVLVIGEG 483 Query: 491 ELMGTLDRSEATQEKVMQLA 510 L G +QE V+ A Sbjct: 484 RLRGDFVNDNLSQETVLAAA 503 Score = 87.8 bits (216), Expect = 9e-22 Identities = 60/237 (25%), Positives = 118/237 (49%), Gaps = 16/237 (6%) Query: 41 DVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPD-AGEIRLRGKPIVFETPLAAQKAG 99 DV VR G +L + G GAG++ L+ I G Y+ G++ L GKP +PL + + G Sbjct: 282 DVSFSVRRGEILGIAGLVGAGRTELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRG 341 Query: 100 IAMIHQELN---LMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAEL------LARLRI 150 + M+ ++ ++P + + +NI L L+ + +AEL + R+R+ Sbjct: 342 LCMVPEDRKHHGIVPDLDVGQNI-----TLTVLNRFSRGSRIDGSAELKTIQDEIGRMRV 396 Query: 151 NL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQ 209 P + +LS +Q +AK + +LI+DEPT + A ++ +I++L Sbjct: 397 KTATPFLPITSLSGGNQQKAVLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKA 456 Query: 210 GKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFP 266 G I+ ++ ++ EV ++D V V +G G D+++ +++++ + + + Q P Sbjct: 457 GLAIIMVSSELAEVLGVSDRVLVIGEGRLRGDFVNDNLSQETVLAAAINQPVPQATP 513 Lambda K H 0.320 0.136 0.381 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: 611 Number of extensions: 26 Number of successful extensions: 9 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: 517 Length of database: 518 Length adjustment: 35 Effective length of query: 482 Effective length of database: 483 Effective search space: 232806 Effective search space used: 232806 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