Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate 8502448 DvMF_3154 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Miya:8502448 Length = 229 Score = 129 bits (324), Expect = 5e-35 Identities = 87/226 (38%), Positives = 125/226 (55%), Gaps = 15/226 (6%) Query: 5 LNFAAVWRDFDTLLAG------LGLGLSLALVSIAIGCVIG---LAMAFALL--SKHRVL 53 + + VWR+FD LL G LG GL++++V +AIG + G L + F LL S L Sbjct: 1 MQWDVVWRNFDYLLVGSWPQGPLG-GLAMSVV-LAIGGIFGAFWLGLGFGLLRLSDRWWL 58 Query: 54 RVLASVYVTVIRNTPILVLILLIYFALPS-LGIRLDKLPSFVITLSLYAGAYLTEVFRGG 112 R+ A +YV +IR P+L+LI YF P LG L + S ++ ++ GAY+ E+ R G Sbjct: 59 RLPAIIYVEIIRGIPLLMLIFWFYFLAPIVLGRTLPEAESALVAFIVFTGAYIAEIVRAG 118 Query: 113 LLSIHKGQREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPE 172 +L++ GQ EA GL + Q YV +P LRN++P+ N F+SL KDTSLA I V E Sbjct: 119 VLALPHGQMEAARGTGLSKSQAMIYVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSE 178 Query: 173 LTYYARKI-NVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLA 217 LT A +I N E E + LY C+ + R E+++A Sbjct: 179 LTRTATQINNRELTAPAELFFTIAVLYFIVCWTLTAASRRMERQMA 224 Lambda K H 0.329 0.142 0.414 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: 141 Number of extensions: 10 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: 220 Length of database: 229 Length adjustment: 22 Effective length of query: 198 Effective length of database: 207 Effective search space: 40986 Effective search space used: 40986 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