Align Inositol transport system permease protein (characterized)
to candidate BPHYT_RS13900 BPHYT_RS13900 ATPase
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__BFirm:BPHYT_RS13900 Length = 385 Score = 390 bits (1003), Expect = e-113 Identities = 205/368 (55%), Positives = 256/368 (69%), Gaps = 5/368 (1%) Query: 4 APTQFAEDERIKTRSKFREAMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQI 63 AP+ DER++ S+F + RPE I G + VF +F + AG+SGMFN GVMNWSQ+ Sbjct: 20 APSLPDSDERLRKESRFGHVLNRPEFAAISGAVLVFLVFALTAGNSGMFNLDGVMNWSQV 79 Query: 64 SAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAI 123 SA I+AVGACLLMIAGEFDLS+GSMIGF+GM++AI SV WP+ LAIL FA + + Sbjct: 80 SAYLGILAVGACLLMIAGEFDLSIGSMIGFSGMMVAIPSVYFHWPISLAILFAFAGSMLL 139 Query: 124 GALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLA-ALF 182 GALNG++V+RT LPSFIVTLAFLFILRG + L +TI+ GV D A+ DW A LF Sbjct: 140 GALNGYLVMRTRLPSFIVTLAFLFILRGLTLALSIMFADRTIVSGVGDLAQQDWFANTLF 199 Query: 183 GGKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGN 242 G L GLF +G + + G +V G+P +I+W + L + +L KTR GN Sbjct: 200 HGVALNGLFTMLARHGIGTMLD----NGHALVPGIPKVILWWLGLAAVCAFVLAKTRAGN 255 Query: 243 WIFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEA 302 WI A GGDA AA+N GVPV RVKI +F+ TAFC+ +FA QV + G A +DRGL KEFEA Sbjct: 256 WILAVGGDANAAKNVGVPVRRVKISLFVLTAFCSCLFAVLQVCDIGSAAADRGLQKEFEA 315 Query: 303 IIAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILN 362 IIA VIGG LLTGGYGSV+GA GALIFGVVQ G+ + V S FRVFLG++LL AV+ N Sbjct: 316 IIAAVIGGTLLTGGYGSVVGACFGALIFGVVQIGITYTNVSSDWFRVFLGVMLLIAVLFN 375 Query: 363 TYIRRVIT 370 Y+RR ++ Sbjct: 376 HYVRRRVS 383 Lambda K H 0.330 0.145 0.443 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: 541 Number of extensions: 32 Number of successful extensions: 2 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: 373 Length of database: 385 Length adjustment: 30 Effective length of query: 343 Effective length of database: 355 Effective search space: 121765 Effective search space used: 121765 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 (21.8 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