Align Inositol transport system permease protein (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 136 bits (342), Expect = 1e-36 Identities = 113/375 (30%), Positives = 179/375 (47%), Gaps = 43/375 (11%) Query: 2 SDAPTQFAEDERIKTR--SKFREAM-IRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVM 58 S +P A+ ++ +T S+F+ + + P L +I + +F + G S F+ + Sbjct: 12 SGSPEAVADFDQGETSFISRFQHMLHVTPSLVPLIVLVLSVIVFGLLLG-SKFFSPFAL- 69 Query: 59 NWSQISAQFMIIAVGAC---LLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILV 115 + I Q I+ + AC L+++ DLSVG+++ + +++ F+ G P +A+ Sbjct: 70 --TLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMVLSSVVMGQFTFRYGLPPEVAVAC 127 Query: 116 TFAIATAIGALNGFIVVRTGLPSFIVTLAF--LFILRGFAIYLPQTIERKTIIGGVADAA 173 T G +NG++V R LP FIVTL + + F +TI +TI AA Sbjct: 128 GLICGTICGFINGWLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRSQTI------AA 181 Query: 174 EGDWLAALFGGKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHV 233 E L LFG KI G AVF G +++ ++LV++ Sbjct: 182 EAP-LLQLFGEKIKIGG----------AVFTYG--------------VIFMVILVVLLAY 216 Query: 234 ILTKTRFGNWIFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSD 293 +L T +G ++A G D EAA SGV V RV I ++M + + G Sbjct: 217 VLRHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPT 276 Query: 294 RGLLKEFEAIIAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGL 353 G L E+I AVVIGG L GG GS+LG GALI GV GL G ++ + +GL Sbjct: 277 SGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGADAQWTYLLIGL 336 Query: 354 ILLFAVILNTYIRRV 368 +++ AV ++ +IR+V Sbjct: 337 LIIAAVAVDQWIRKV 351 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: 444 Number of extensions: 24 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: 353 Length adjustment: 29 Effective length of query: 344 Effective length of database: 324 Effective search space: 111456 Effective search space used: 111456 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: 49 (23.5 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