Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_05500 (242 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 117 bits (293), Expect = 2e-31 Identities = 74/228 (32%), Positives = 121/228 (53%), Gaps = 12/228 (5%) Query: 11 LSAFSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLI 70 + AFS F LL W T+ LSA++ + +GL+ A A+ S +K +R+ A Y L Sbjct: 1 IRAFSYNEFLFLLSAVQW-TLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLF 59 Query: 71 RGVPDLVLMLLIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAI 130 +G P L+ + L+F+ ++++P+ A + L A+ E +RG I Sbjct: 60 QGTPLLMQLFLVFFGATVM-----------GLDLNPWAAAALGLTLNASAFLGEIWRGCI 108 Query: 131 LAVPRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADL 190 AVPRGQ EAA+A GL+ R+V+ PQ ++ A+P + ++K+T+L +IIG +L Sbjct: 109 QAVPRGQWEAASALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTEL 168 Query: 191 VKAAQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAR 238 +A Q +T+Q F + A++Y L+ + + LERRYA R Sbjct: 169 TRAGQIVNNATFQPFLVFGIVAVLYFLMCWPLSLLSARLERRYALATR 216 Lambda K H 0.329 0.142 0.423 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: 138 Number of extensions: 6 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: 242 Length of database: 216 Length adjustment: 23 Effective length of query: 219 Effective length of database: 193 Effective search space: 42267 Effective search space used: 42267 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: 46 (22.3 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