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 RR42_RS02575 RR42_RS02575 ABC transporter
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__Cup4G11:RR42_RS02575 Length = 299 Score = 365 bits (936), Expect = e-106 Identities = 182/296 (61%), Positives = 229/296 (77%), Gaps = 5/296 (1%) Query: 8 LSTAIVAA--LLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSY-LGTEPGKPIGYS 64 L++ ++AA L A++LTGTL+KIK+TG ITLG R++SIPF+Y LG + +GYS Sbjct: 6 LASLMIAAGVLCGTAQAAEQLTGTLQKIKDTGVITLGVRESSIPFNYNLGGV--RQVGYS 63 Query: 65 HDLQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDF 124 +D+ +K+VEA+K +L LP L+V+ +TSQ RI L+QNGT+DIECGSTTNN ERQKQ F Sbjct: 64 YDINVKIVEAIKDQLKLPNLQVKEIPITSQNRITLLQNGTIDIECGSTTNNLERQKQASF 123 Query: 125 SVGIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKD 184 + IF +GTR++ KK IKD+ DLKGKNVVTTAGTTSERLL+ MN D+K+GMNIIS KD Sbjct: 124 TTSIFIIGTRIMVKKDGGIKDWADLKGKNVVTTAGTTSERLLRKMNDDQKLGMNIISTKD 183 Query: 185 HGESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFK 244 HG+SF+ LESGRAVAFMMDDALL+GE AKAK P DW+V G PQS E YGCM+RK DA FK Sbjct: 184 HGQSFLTLESGRAVAFMMDDALLFGERAKAKNPADWIVVGKPQSRESYGCMIRKDDAQFK 243 Query: 245 KVVDKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDKAAE 300 K+ D IT G +N +Y KWF QP+PPKGLNL+FP+SE++K L +P DKA + Sbjct: 244 KLSDTVITGMMKDGSINTLYTKWFQQPVPPKGLNLDFPLSEDMKALFKTPNDKALD 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: 308 Number of extensions: 4 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: 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