Align ABC transporter related (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 228 bits (581), Expect = 4e-64 Identities = 147/472 (31%), Positives = 258/472 (54%), Gaps = 13/472 (2%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 ++ L I K + V+A D++L + G + ALLGENGAGKSTL+ ++ G +D G I+ Sbjct: 29 VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 G P F +P DA +AGI VYQ LV ++TVA+N+ LG P L+ +M + A Sbjct: 89 DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDM--LLRPARMRDEVAA 146 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 + ++ L +D +A + S+ +Q + I + + ++VL+LDEPTA L +E LF + Sbjct: 147 LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAM 206 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELP-QPKLIEAMLGRSLQ 242 ++ +G A+VFI+H L +V ++D I +LR G+ + E+ A++P Q L M+GR + Sbjct: 207 WRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDVV 266 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 Q+ K+ +T + V LS+E +S G + ++L V +G+ V +AG+ G+G+ E+ Sbjct: 267 LQVDAKR-----LTPVDTV-LSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKELVE 319 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362 A+ GL ++G + + G+ G+A PEDR+ L + +N +L + Sbjct: 320 AICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTR 379 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 + +L T + + + + D P LSGGN QK+++ R +P ++ Sbjct: 380 NQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVI 439 Query: 423 VLDEPTRGIDIGAHAEI-VKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 V + PT+G+DI A E+ +L+ G +L+ + +L+E + ++++ V+ Sbjct: 440 VAENPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVM 489 Score = 66.6 bits (161), Expect = 2e-15 Identities = 56/239 (23%), Positives = 114/239 (47%), Gaps = 11/239 (4%) Query: 255 VTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGS 314 V R + + S V I L + G L G G+G+S + + + G D+G+ Sbjct: 29 VVRLDGICKSFGKVRANHDI---TLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGT 85 Query: 315 IHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNT 374 I + G + P DA+ AGI + + + + +++ EN++L + L Sbjct: 86 IVVDGVPTVFASPRDALRAGIGMVYQHFML---VDSMTVAENVLLGQSPDM----LLRPA 138 Query: 375 RQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIG 434 R ++ ++ +A A + + LS G +Q+V + + L + +L+LDEPT + Sbjct: 139 RMRDEVAALAERYGLAVDPAAR-VGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPR 197 Query: 435 AHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVM 493 ++ + + + D+G +L+ S +L E++ ++++ +LR V E S A++ +Q V+ Sbjct: 198 ETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVL 256 Score = 64.3 bits (155), Expect = 1e-14 Identities = 58/219 (26%), Positives = 103/219 (47%), Gaps = 18/219 (8%) Query: 12 KHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEP--QH 69 +H G L DVSL++ GE+ A+ G G G+ LV+ + G + G++ LG P + Sbjct: 284 EHLSGA-GLSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREF 342 Query: 70 FNTP--------MDAQKAGISTVYQEVNLVPN-LTVAQNLFLGYEPRRLGLIHFKKMYAD 120 F P + + G++T + ++LV N L +N F + + L + A Sbjct: 343 FAGPPGRRGLAYIPEDRQGLATC-RHLDLVDNFLLTTRNQFA----KGVFLDRTEATNAV 397 Query: 121 ARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF 180 R V D++AP S Q + I R +V+V + PT LD + ++ Sbjct: 398 KRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVW 457 Query: 181 GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFI 219 G L + ++ ++ +T L++ +++DRI V+ G+FI Sbjct: 458 GRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFI 495 Lambda K H 0.319 0.136 0.377 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: 622 Number of extensions: 39 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 499 Length of database: 537 Length adjustment: 35 Effective length of query: 464 Effective length of database: 502 Effective search space: 232928 Effective search space used: 232928 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