Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Ga0059261_2250 Ga0059261_2250 ABC-type multidrug transport system, ATPase component
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Korea:Ga0059261_2250 Length = 307 Score = 117 bits (292), Expect = 8e-31 Identities = 91/295 (30%), Positives = 143/295 (48%), Gaps = 10/295 (3%) Query: 3 ATLRFDNIGKVFPGVR-ALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRV 61 A + + + KV+ G + ALD VSF V GQ+ GL+G NGAGKSTL+ IL G +GR Sbjct: 4 AAIEIEGLSKVYQGGKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRA 63 Query: 62 MIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFV 121 I G ++ + A GI ++QE+ + P T E L + G +A+R Sbjct: 64 SIWGFDIDQHPRNAKRAIGI--VNQEILFDPFFTPVETLEI-----QAGLYGVPKAQRRS 116 Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181 E L A+ + +A R LS ++ + + KA++ + V+ LDEPT+ + + L+ Sbjct: 117 MELLRAVHLEDKAHAYSRTLSGGMKRRLMVAKAMVHSPPVLVLDEPTAGVDIELRQQLWA 176 Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLE--GVTRDTIVSEMVG 239 VR L ++ +H ++E ELCD I G+ IA+ PT E G T++ V V Sbjct: 177 YVRSLNERGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAVEVTVD 236 Query: 240 REISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSE 294 R+I+ + + EV+ + +A Q + EV FG+V E Sbjct: 237 RDIAAVPDSRCFQKIEVKGDRTLVITYAKDQANAGEVLGAVQAAGFGIVDVSTRE 291 Score = 71.6 bits (174), Expect = 4e-17 Identities = 59/246 (23%), Positives = 118/246 (47%), Gaps = 22/246 (8%) Query: 265 GHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKV--RSA 322 G SF V RG+I G G GAG+S L++++ G +K G + G I R+A Sbjct: 18 GKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRASIWGFDIDQHPRNA 77 Query: 323 GEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAETADRFIKL 382 AI GIV + + ++ G++ K + + + ++ Sbjct: 78 KRAI--------------GIVNQEILFDPFFTPVETLEIQAGLYGVPKAQRRSME-LLRA 122 Query: 383 LKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQ 442 + ++ + R LSGG +++ ++++ + V++LDEPT G+D+ + +++ + Sbjct: 123 VHLEDKAHAYS-RTLSGGMKRRLMVAKAMVHSP-PVLVLDEPTAGVDIELRQQLWAYVRS 180 Query: 443 LAERGCAIVMISSELPEVLGVSDRIVVMRQGR-ISGELTRK--DATEQSVLSLALPQSST 499 L ERG +V+ + L E + DRI ++ G+ I+ E TR+ T++ + + + + Sbjct: 181 LNERGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAVEVTVDRDIA 240 Query: 500 ALPGTQ 505 A+P ++ Sbjct: 241 AVPDSR 246 Lambda K H 0.320 0.136 0.385 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: 327 Number of extensions: 17 Number of successful extensions: 4 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: 512 Length of database: 307 Length adjustment: 31 Effective length of query: 481 Effective length of database: 276 Effective search space: 132756 Effective search space used: 132756 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: 50 (23.9 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