Align PP1071, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate Ac3H11_1642 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= TCDB::Q88NY2 (306 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1642 Length = 296 Score = 272 bits (696), Expect = 6e-78 Identities = 141/296 (47%), Positives = 193/296 (65%), Gaps = 6/296 (2%) Query: 9 LGAAIAAAVIASPAMAEELTG--TLKKIKESGTITLGHRDSSIPFSYLAGKPEPVGYSHD 66 L A +AA++ + +A + TLKK+ ESG ITL +R+SS+PFSYL+G PVG++ D Sbjct: 3 LSAVTSAAIVVTGLLASTVVSADTLKKVAESGKITLAYRESSVPFSYLSGPGVPVGFAVD 62 Query: 67 IQLAVVDALKKQLGTD-IKVRYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQVGFSV 125 I AVVDA+KK++ +KV VTSQ RIPL+ NGT+DLECGSTTNN R + V F+V Sbjct: 63 ISNAVVDAVKKRVNNPALKVELQAVTSQNRIPLLTNGTIDLECGSTTNNSVRGKDVQFAV 122 Query: 126 GIFEVGTRLLTKVKDGQPAYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMKMNVISAK 185 F GTRLLTK G K++ DLA K V +T+GTT+ ++++ N D+ + M+++ K Sbjct: 123 NYFYTGTRLLTKKTSG---VKNYADLAKKKVASTSGTTNAQVIRKYNRDQNLDMDIVLGK 179 Query: 186 DHGEAFNMLESGRAVAFMMDDALLAGEMAKARKPADWVITGTPQSYEIYGCMVRKDDAAF 245 DH ++ ++ESGRA AF MDD LL G M R PA+W + G E Y CM+RKDD F Sbjct: 180 DHDDSLLLVESGRAEAFAMDDILLFGLMGNQRNPAEWTVVGDSLQVEPYACMLRKDDPQF 239 Query: 246 KKAVDDAIVAYFKSGEVNKSYEKWFMQPIPPKGLNLNFQMSEELKKLIAEPTDKAA 301 + V+ I KSGE +K Y KWFM P+PP+ NLN MS+EL++ + +DK A Sbjct: 240 QALVNGVIGGMMKSGEFDKLYTKWFMSPVPPRNQNLNLAMSKELRENLVAQSDKPA 295 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: 234 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: 296 Length adjustment: 27 Effective length of query: 279 Effective length of database: 269 Effective search space: 75051 Effective search space used: 75051 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 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