Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate 8502448 DvMF_3154 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Miya:8502448 Length = 229 Score = 101 bits (252), Expect = 2e-26 Identities = 70/215 (32%), Positives = 113/215 (52%), Gaps = 13/215 (6%) Query: 173 WPQTP-GWLV--VILAIALVLFVSWLAQR----QRSPRDWRWLYGAIAVVTV--LMLLTQ 223 WPQ P G L V+LAI + WL + S R W L I V + + LL Sbjct: 18 WPQGPLGGLAMSVVLAIGGIFGAFWLGLGFGLLRLSDRWWLRLPAIIYVEIIRGIPLLML 77 Query: 224 LSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALG 283 + W L P + R E + L+ + +TGA+I EI+R G+L++P GQ EAA G Sbjct: 78 IFWFYFLAPIVLG---RTLPEAESALVAFIVFTGAYIAEIVRAGVLALPHGQMEAARGTG 134 Query: 284 LTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATA-QTTLNQTGRP 342 L++SQ + +++PQALR ++PS +Q+V K++SLA +G +L TA Q + P Sbjct: 135 LSKSQAMIYVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSELTRTATQINNRELTAP 194 Query: 343 VEVFLILMLTYLAINAVISAGMNGLQQRLQRWGVR 377 E+F + + Y + ++A +++++ R+ R Sbjct: 195 AELFFTIAVLYFIVCWTLTAASRRMERQMARYQAR 229 Score = 37.0 bits (84), Expect = 5e-07 Identities = 31/88 (35%), Positives = 48/88 (54%), Gaps = 8/88 (9%) Query: 72 YRTADSYARALVVGLVNSLRVIAIGLILTTV-IGTLAGVAAFSENWLLRQLSRGYVAVVR 130 Y S+ + + GL S+ V+AIG I +G G+ S+ W LR + YV ++R Sbjct: 12 YLLVGSWPQGPLGGLAMSV-VLAIGGIFGAFWLGLGFGLLRLSDRWWLRLPAIIYVEIIR 70 Query: 131 NTPLLLQLIVWYF---PILL--SLPAAQ 153 PLL+ LI W++ PI+L +LP A+ Sbjct: 71 GIPLLM-LIFWFYFLAPIVLGRTLPEAE 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: 226 Number of extensions: 10 Number of successful extensions: 2 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: 229 Length adjustment: 26 Effective length of query: 351 Effective length of database: 203 Effective search space: 71253 Effective search space used: 71253 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