Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__HerbieS:HSERO_RS22215 Length = 323 Score = 120 bits (300), Expect = 6e-32 Identities = 89/307 (28%), Positives = 153/307 (49%), Gaps = 19/307 (6%) Query: 19 LLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVG 78 LL + +V+++ + F+ ++ ++ +LAL ML +++ GIDLS Sbjct: 1 LLALLTVVLILLVGVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTR--GIDLSVAS 58 Query: 79 LANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCT 138 LSGM++A+L P L +F + +++GL+ GLLNG +I L L PI+ T Sbjct: 59 NLALSGMMSALLAMHF------PALPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVT 112 Query: 139 LGTQLLFTGFAVVISNGASVH-----VDYVE-PLSDIGNGTVLQVPIAFCIFLAAVIVLG 192 LG+ ++ G V+S GA V D++ PL+ +G T L + AV+ + Sbjct: 113 LGSMSVYRGMVFVLSGGAWVSSRNMPADFIAFPLARLGGLTHL-----VWLGALAVVAIW 167 Query: 193 WLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKW 252 +L + + FG LY +G +P AA Y GI L+ TY + G +A LAG + + A Sbjct: 168 FLARHTRFGRDLYAIGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYT 227 Query: 253 DYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWG 312 + + L I V+GGV+ AGG G++ A L +++ ++ +S F+ G Sbjct: 228 EIAYGFELTVIAACVIGGVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTG 287 Query: 313 FLLLLSL 319 ++L ++ Sbjct: 288 LVILCAV 294 Lambda K H 0.327 0.143 0.429 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: 308 Number of extensions: 19 Number of successful extensions: 3 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: 357 Length of database: 323 Length adjustment: 28 Effective length of query: 329 Effective length of database: 295 Effective search space: 97055 Effective search space used: 97055 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: 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