Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate 207827 DVU2340 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= uniprot:Q31RP0 (377 letters) >MicrobesOnline__882:207827 Length = 230 Score = 105 bits (263), Expect = 9e-28 Identities = 69/203 (33%), Positives = 111/203 (54%), Gaps = 10/203 (4%) Query: 182 VILAIALVLFVSWLAQRQRSPR-DWRWLYGAIAVVTV-----LMLLTQLSWPQQLQPGQI 235 ++LAI + WL R +W A A+V V + LL + W L P + Sbjct: 30 ILLAIGGIFGAFWLGLAFGLMRLSEKWWVRAPAIVYVEVIRGIPLLMLIFWFYFLAPIAL 89 Query: 236 RGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVV 295 L E + L+ + +TGA+I EI+R G+L++PAGQ EAA GL+++Q + +++ Sbjct: 90 GHTLP---EAESALIAFIVFTGAYIAEIVRAGVLALPAGQMEAARGTGLSKTQAMLFVIL 146 Query: 296 PQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQT-GRPVEVFLILMLTYL 354 PQALR ++PS +Q+V K++SLA +G +L TA N+T P E+FL + L Y Sbjct: 147 PQALRNMIPSFVNQFVSLTKDTSLAYIIGVSELTRTATQVNNRTLTAPTEIFLTIALMYF 206 Query: 355 AINAVISAGMNGLQQRLQRWGVR 377 I V++A L++++ R+ R Sbjct: 207 VICWVLTATSRRLEKQMARYQAR 229 Score = 38.5 bits (88), Expect = 2e-07 Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 6/87 (6%) Query: 72 YRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRN 131 Y SY + G+ S+ + G+ +G G+ SE W +R + YV V+R Sbjct: 12 YLLVGSYPDGPLGGMAMSILLAIGGIFGAFWLGLAFGLMRLSEKWWVRAPAIVYVEVIRG 71 Query: 132 TPLLLQLIVWYF---PILL--SLPAAQ 153 PLL+ LI W++ PI L +LP A+ Sbjct: 72 IPLLM-LIFWFYFLAPIALGHTLPEAE 97 Lambda K H 0.326 0.140 0.445 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: 214 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 230 Length adjustment: 26 Effective length of query: 351 Effective length of database: 204 Effective search space: 71604 Effective search space used: 71604 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: 48 (23.1 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