Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 313 bits (803), Expect = 7e-90 Identities = 187/473 (39%), Positives = 271/473 (57%), Gaps = 7/473 (1%) Query: 6 HQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGT 65 ++ +L GL K + L V SLR GE++AL GENGAGKSTL K ++G+ G Sbjct: 13 NEVVLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGH 71 Query: 66 IWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKR 125 + GQA +P + A++LG+ V QE+NLLP ++VA+NLF+ P RFG + K + + Sbjct: 72 MTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQL 131 Query: 126 ATELMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELL 184 AT MA G ++D P+ + QQ+V I R + VLILDEPTA L +EV LL Sbjct: 132 ATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALL 191 Query: 185 FDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR 244 F + +LR RGV++++++H L+++ +V+ RI VLR+G V ELV +M+GR Sbjct: 192 FTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGR 251 Query: 245 ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304 EL H GR L P+ + + EVR GEI G++GL+G+GRTE Sbjct: 252 ELGEHI--DLGRRQLG-APLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLR 308 Query: 305 VIFGIKPADSGTALIKGKPQ--NLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA 362 +I+G ADSG + PQ ++ SP A GI EDRK +G++ S+ NI L Sbjct: 309 LIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALG 368 Query: 363 LQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422 + + ++ +AER I+ + IR+ +Q + LSGGNQQKV++ RWL Q Sbjct: 369 NLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQ 428 Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475 L+ DEPTRGIDVGA +I L+ L G AL+V+SS+L EL+ DR+ ++ Sbjct: 429 VLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVL 481 Score = 96.3 bits (238), Expect = 2e-24 Identities = 70/242 (28%), Positives = 125/242 (51%), Gaps = 10/242 (4%) Query: 259 LSDKPVAAFKNYGK---KGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSG 315 L+++ V A GK + + L +R GE++ L G G+G++ +++I G++ +G Sbjct: 11 LANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTG 70 Query: 316 TALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA-LQAQRGWLRPIS 374 +G+ S +A LG+ ++ ++ +V EN+ L L ++ GW IS Sbjct: 71 HMTYRGQAYAPGSRGEAERLGVRMVMQELN---LLPTLTVAENLFLDNLPSRFGW---IS 124 Query: 375 RKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGID 434 K +++A + ++G+ + P+ L G+QQ V ++R L+ LILDEPT + Sbjct: 125 HKRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLT 184 Query: 435 VGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494 A + IE L A G+A++ IS LEEL A R++++RD K V + P+ S + Sbjct: 185 AREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAEL 244 Query: 495 MN 496 +N Sbjct: 245 VN 246 Score = 75.1 bits (183), Expect = 6e-18 Identities = 62/206 (30%), Positives = 101/206 (49%), Gaps = 10/206 (4%) Query: 28 VDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL--EGQAISPKNTAHAQQLG 85 V F +R GEI + G GAG++ L++ + G AD G I L QA+S + A + G Sbjct: 283 VSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAG 342 Query: 86 IGTVYQE---VNLLPNMSVADNLFIGR--EPKRFGLLRRKEMEKRATE--LMASYGFSLD 138 I + ++ LL S++ N+ +G R G+L E EK E + A S Sbjct: 343 IALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLD-SEAEKALAERQIQAMRIRSAG 401 Query: 139 VREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSL 198 ++ + S QQ V I R ++ +VL+ DEPT +D ++ L+ +L +G +L Sbjct: 402 AQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKAL 461 Query: 199 IFVTHFLDQVYQVSDRITVLRNGSFV 224 + V+ L ++ + DRI VL G + Sbjct: 462 VVVSSDLRELMLICDRIAVLSAGRLI 487 Lambda K H 0.321 0.138 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: 592 Number of extensions: 30 Number of successful extensions: 8 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: 500 Length of database: 524 Length adjustment: 35 Effective length of query: 465 Effective length of database: 489 Effective search space: 227385 Effective search space used: 227385 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