Align PP1071, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_028312342.1 H566_RS0116805 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q88NY2 (306 letters) >NCBI__GCF_000482785.1:WP_028312342.1 Length = 307 Score = 250 bits (638), Expect = 3e-71 Identities = 142/293 (48%), Positives = 180/293 (61%), Gaps = 4/293 (1%) Query: 12 AIAAAVIASPAMAEELTGTLKKIKESGTITLGHRDSSIPFSYLAGKPEPVGYSHDIQLAV 71 A+ AA+ A A A+ELTGTLKKIK++G +T+G RDSS SY G + G+ ++ + Sbjct: 12 AVGAALAAHGASAQELTGTLKKIKDTGKVTMGVRDSSGVLSYTLGNGQYAGFHVNLCQNL 71 Query: 72 VDALKKQLGTD-IKVRYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQVGFSVGIFEV 130 + L+KQL + + Y VTS RIPLV+NGTVDLECGSTTNNV RQ+QV F + + Sbjct: 72 LADLQKQLKLPKLNIEYMSVTSSNRIPLVENGTVDLECGSTTNNVARQKQVAFGLTTYVT 131 Query: 131 GTRLLTKVKDGQPAYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMKMNVISAKDHGEA 190 R+ V+ GQ Y L GK V TT GTTS + L+ + +K N + KDH E+ Sbjct: 132 EVRMA--VRAGQRLYS-VAQLDGKTVATTTGTTSVQTLRKSERGQNIKFNEVYGKDHAES 188 Query: 191 FNMLESGRAVAFMMDDALLAGEMAKARKPADWVITGTPQSYEIYGCMVRKDDAAFKKAVD 250 F +LESGRA AF+MDD +LAG +A ++ P + I G P S E M RKDD AFK AVD Sbjct: 189 FLLLESGRADAFVMDDYILAGNIANSKDPKQFDIVGEPLSVEPIAIMFRKDDPAFKTAVD 248 Query: 251 DAIVAYFKSGEVNKSYEKWFMQPIPPKGLNLNFQMSEELKKLIAEPTDKAADE 303 D I KSGE K Y KWFM PIPPK N MS+ LK IA P DK ++ Sbjct: 249 DYIRKTMKSGEFEKLYNKWFMSPIPPKNNNPGVPMSQRLKDAIANPNDKPMED 301 Lambda K H 0.315 0.131 0.366 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: 241 Number of extensions: 7 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: 306 Length of database: 307 Length adjustment: 27 Effective length of query: 279 Effective length of database: 280 Effective search space: 78120 Effective search space used: 78120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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