Align Probable binding protein component of ABC transporter, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate Dsui_0635 Dsui_0635 periplasmic component of amino acid ABC-type transporter/signal transduction system
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__PS:Dsui_0635 Length = 299 Score = 384 bits (987), Expect = e-111 Identities = 198/301 (65%), Positives = 238/301 (79%), Gaps = 3/301 (0%) Query: 1 MRIAPSLLSTAIV-AALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGK 59 MR +L + A++ +AL +APV+A E + TLKKIK+TG+ITLGHR++SIPFSY + + Sbjct: 1 MRKTLTLAAAAVIGSALCAAPVLAQE-SPTLKKIKDTGSITLGHRESSIPFSYYDDKQ-Q 58 Query: 60 PIGYSHDLQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQ 119 IGYSH++ LK V+A+K EL L +L V+ VTS RI L+QNGTVD+ECGSTTNN ERQ Sbjct: 59 VIGYSHEMMLKAVDAIKAELKLAKLDVKLMPVTSANRITLLQNGTVDMECGSTTNNLERQ 118 Query: 120 KQVDFSVGIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNI 179 KQV FS IF +GTRL++KK A +KDF DL GKNVVTTAGTTSERL++ MN +K+M MNI Sbjct: 119 KQVGFSTSIFVIGTRLMAKKDAGVKDFPDLAGKNVVTTAGTTSERLIRKMNEEKQMKMNI 178 Query: 180 ISAKDHGESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKG 239 ISAKDHGESF+ LESGRAVAFMMDDALLYGEMAKAK+P DWVV GT QS E YGCM+RK Sbjct: 179 ISAKDHGESFLTLESGRAVAFMMDDALLYGEMAKAKRPGDWVVVGTAQSKEAYGCMLRKD 238 Query: 240 DAAFKKVVDKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDKAA 299 DA FKKVVD A+T SGE KIY+KWF PIPPKGLNLN P+S+++K L +P DKA Sbjct: 239 DAGFKKVVDAALTKAMTSGEAEKIYNKWFMNPIPPKGLNLNMPLSDDMKALYKAPNDKAY 298 Query: 300 E 300 E Sbjct: 299 E 299 Lambda K H 0.314 0.132 0.370 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: 316 Number of extensions: 6 Number of successful extensions: 2 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: 302 Length of database: 299 Length adjustment: 27 Effective length of query: 275 Effective length of database: 272 Effective search space: 74800 Effective search space used: 74800 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: 42 (22.0 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