Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 431 bits (1107), Expect = e-125 Identities = 228/503 (45%), Positives = 330/503 (65%), Gaps = 8/503 (1%) Query: 20 IPVD--EPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIY 77 IPVD + LL++ + K F +ALSD+ L +RPG + ALMGENGAGKSTLMK+++G++ Sbjct: 1 IPVDMTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVH 60 Query: 78 QPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMID 137 PD GE+ L G+PV P A+ AGI +I+QEL + P++S+A N+++G E +ID Sbjct: 61 APDQGEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLID 120 Query: 138 HREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITD 197 H M T +L +L + G LSIAE+Q VEIA+A+ + S I+IMDEPT+A+++ Sbjct: 121 HAAMRSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSE 180 Query: 198 KEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLI 257 +E LF+++ L+ +G IIYI+H+M EV+++AD V V RDG+++G D +D + ++ Sbjct: 181 RETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIV 240 Query: 258 SMMVGRELSQLFPVREKPIGD-----LLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMG 312 MMVGR LS+ + + D +M VR L G + SFD+ AGE+LG AGL+G Sbjct: 241 QMMVGRSLSEFYQHQRIAPADAAQLPTVMQVRAL-AGGKIRPASFDVRAGEVLGFAGLVG 299 Query: 313 SGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVL 372 +GRT +A +FG P GG+I L+G+PV I P A+ G A + EDRK GLF ++V Sbjct: 300 AGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVA 359 Query: 373 ENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARW 432 N M V + G ++ ++L + ++L VK E + LSGGNQQK LLARW Sbjct: 360 ANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARW 419 Query: 433 LMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMH 492 L P++LILDEPTRG+D+ AK+EIY+L+ LAS+G+AV++ISSELPEV+G+ DRV+VM Sbjct: 420 LEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMR 479 Query: 493 EGDLMGTLDRSEATQERVMQLAS 515 EG + G L + TQE +M+LA+ Sbjct: 480 EGMITGELAGAAITQENIMRLAT 502 Score = 105 bits (263), Expect = 3e-27 Identities = 67/221 (30%), Positives = 117/221 (52%), Gaps = 5/221 (2%) Query: 299 LHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTE 358 + GEI + G G+G++ + + + G+ D GEI LDG+PV + DP + G L+ + Sbjct: 33 IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 92 Query: 359 DRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDT 418 + ++ P +SV N+ M G I A+R+ + + ++L + + Sbjct: 93 ELAVA---PNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASDLA-GR 147 Query: 419 LSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSEL 478 LS QQ+ +AR L+ RI+I+DEPT + +++ ++ L EG+A+I IS + Sbjct: 148 LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRM 207 Query: 479 PEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519 EV ++DRV V+ +G +G L R E ER++Q+ G S+ Sbjct: 208 AEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 248 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: 22 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 502 Length adjustment: 35 Effective length of query: 486 Effective length of database: 467 Effective search space: 226962 Effective search space used: 226962 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