Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Pedo557:CA265_RS01275 Length = 462 Score = 328 bits (840), Expect = 3e-94 Identities = 181/451 (40%), Positives = 257/451 (56%), Gaps = 12/451 (2%) Query: 22 FVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISG 81 F+ LI+ A LGG L+G+D AV+SG I LK Y LS EGL +S ++G +VGV SG Sbjct: 9 FIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSG 68 Query: 82 FLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEA 141 +LSD+ GRRK+L AA+LF +SA+ A S LI R++ G+G+G+ S++S YI+E Sbjct: 69 YLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEV 128 Query: 142 APPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTG----------WRWMLA 191 AP RG L YQL +GI A Y NL +QR T G G WR M Sbjct: 129 APSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFI 188 Query: 192 YGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQ 251 G+VP+ F L+LL+VPESPRWL + G+ EAL L +ING + EL +I+ + ++ Sbjct: 189 VGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKINGAETGRLELDSIK-EMASQK 247 Query: 252 MGSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVG 311 G +L + L K L + +L +Q G+N + +YGP I K G + I+G Sbjct: 248 SGGYKELMRLPLSKLLALATILTALSQFSGINGVIFYGPTILKSAGIVTSDALFYQVILG 307 Query: 312 VVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVA 371 V+FT IA+ +D GR+ L IGS A + L G F ++T M+ +IL F+ Sbjct: 308 SANVLFTFIAISKVDTWGRRPLYIIGSLCAAGALALTGFCFLMDITGWFMLFSIIL-FLL 366 Query: 372 AFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWI 431 F S+GP+ +++ +EIFP H+R A + + +W ++W + P+M D G+A TF+I Sbjct: 367 FFAFSLGPLKFVISTEIFPTHIRGTALSMCIMTMWVSDWVVNMLFPIMRDGLGIATTFFI 426 Query: 432 FAVINILCFLFVVTICPETKNKSLEEIEKLW 462 F+ IL FL+ ETK KSLEEIEK W Sbjct: 427 FSFFCILSFLYAKKKLFETKGKSLEEIEKAW 457 Lambda K H 0.327 0.142 0.425 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: 577 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 462 Length adjustment: 33 Effective length of query: 431 Effective length of database: 429 Effective search space: 184899 Effective search space used: 184899 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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