Align Inositol transport system ATP-binding protein (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 336 bits (862), Expect = 1e-96 Identities = 185/475 (38%), Positives = 294/475 (61%), Gaps = 4/475 (0%) Query: 39 LADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKA 98 L +V L +R G VLAL GENGAGKSTL K+I+G+ P G + RG+ + A++ Sbjct: 31 LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERL 90 Query: 99 GIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLARLRIN-LDPEEQ 157 G+ M+ QELNL+P +++AEN+++ + ++H+ + + +AR+ ++ +DP+ Sbjct: 91 GVRMVMQELNLLPTLTVAENLFLDNLP-SRFGWISHKRLRQLATAAMARVGLDAIDPDTP 149 Query: 158 VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYIT 217 VG L I +QMVEIA+ + D +LI+DEPT+ +T +EVA LF+ I L+++G IVYI+ Sbjct: 150 VGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYIS 209 Query: 218 HKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLL 277 H++ E+ +A + V RDG + + +S L+++MVGREL + L +G LL Sbjct: 210 HRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLGRRQLGAPLL 269 Query: 278 TVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITL--DGKA 335 V L ++VSF++ AGEI GI+GL+G+GRT + I+G + SG I L +A Sbjct: 270 KVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQA 329 Query: 336 VRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCE 395 V I P A+ G AL+TEDRK GL S+ N+ + L + G + +A +AL E Sbjct: 330 VSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAE 389 Query: 396 DMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYR 455 + +R+++ +Q + LSGGNQQK ++ RWL + ++L+ DEPTRGIDVGAK +IY Sbjct: 390 RQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYG 449 Query: 456 LIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLA 510 L+A LA +G A++++SS+L E++ + DR+ V+ G L+ T R +Q++++ A Sbjct: 450 LLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAA 504 Score = 88.6 bits (218), Expect = 5e-22 Identities = 60/207 (28%), Positives = 109/207 (52%), Gaps = 5/207 (2%) Query: 287 VFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIE 346 V +VS L AGE+L + G G+G++ +++ I G+ ++G +T G+A A Sbjct: 30 VLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAER 89 Query: 347 KGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTP 406 G ++ ++ L P L+V EN+ + LP + G+I K LR L ++ + Sbjct: 90 LGVRMVMQE---LNLLPTLTVAENLFLDNLP--SRFGWISHKRLRQLATAAMARVGLDAI 144 Query: 407 SLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMA 466 + + L G+QQ +AR L+ + +LILDEPT + A ++ I L + G+A Sbjct: 145 DPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVA 204 Query: 467 VIMISSELPEVLGMSDRVMVMHEGELM 493 ++ IS L E+ ++ R++V+ +G+L+ Sbjct: 205 IVYISHRLEELQRVAQRIVVLRDGKLV 231 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: 28 Number of successful extensions: 8 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: 524 Length adjustment: 35 Effective length of query: 482 Effective length of database: 489 Effective search space: 235698 Effective search space used: 235698 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