Align Inositol transport system ATP-binding protein (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 271 bits (694), Expect = 3e-77 Identities = 168/494 (34%), Positives = 274/494 (55%), Gaps = 14/494 (2%) Query: 21 PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEI 80 P ++ + I K F V A D+ L +RPG + AL+GENGAGKSTLM I+AG + DAG I Sbjct: 27 PPVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTI 86 Query: 81 RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRC 140 + G P VF +P A +AGI M++Q L+ M++AEN+ +G+ L R+ Sbjct: 87 VVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRPARMRDE--- 143 Query: 141 TAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLF 200 A L R + +DP +VG LS+ ERQ VEI K + DS +LI+DEPT+ +T +E LF Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203 Query: 201 SIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGR 259 + + QGK +V+I+HK+ EV +ADE+A+ R G + AD N L + MVGR Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263 Query: 260 E-LSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETI 318 + + Q+ R TP+ D +L+V L+ G+ DVS + GEI+ IAG+ G+G+ + E I Sbjct: 264 DVVLQVDAKRLTPV-DTVLSVEHLSGAGL-SDVSLQVRRGEIVAIAGVAGNGQKELVEAI 321 Query: 319 FGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPC--LSVLENMEMAVL 376 G+ +G++ + G+ R +G A + EDR+ GL C L +++N + Sbjct: 322 CGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQ--GLATCRHLDLVDNFLLTTR 379 Query: 377 PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLL 436 + F+ + + + + V+ + LSGGN QK ++ R P ++ Sbjct: 380 NQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVI 439 Query: 437 ILDEPTRGIDVGAKAEIY-RLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495 + + PT+G+D+ A E++ RL+ ++ G V++++ +L E L ++DR+ VM+ G + Sbjct: 440 VAENPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVMYRGRFIDV 497 Query: 496 LDRSEATQEKVMQL 509 D+ + + + + L Sbjct: 498 FDKDDTAKVQAIGL 511 Score = 68.6 bits (166), Expect = 6e-16 Identities = 52/224 (23%), Positives = 100/224 (44%), Gaps = 6/224 (2%) Query: 39 LADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKA 98 L+DV L+VR G ++A+ G G G+ L++ I G+ +P+AGE+R+ G+P + Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350 Query: 99 GIAMI---HQELNLMPHMSIAENIWIG-REQLNSLHMVNHREMHRCTAELLARLRINL-D 153 G+A I Q L H+ + +N + R Q ++ E ++ + D Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGD 410 Query: 154 PEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGI 213 LS Q + I + ++++ + PT + ++ + + +S G+ Sbjct: 411 ITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GV 469 Query: 214 VYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257 + +T +NE +AD +AV G +I + D I +M+ Sbjct: 470 LLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 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: 580 Number of extensions: 30 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: 537 Length adjustment: 35 Effective length of query: 482 Effective length of database: 502 Effective search space: 241964 Effective search space used: 241964 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