Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 209487 DVU0548 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= uniprot:Q1MCU0 (300 letters) >MicrobesOnline__882:209487 Length = 302 Score = 276 bits (707), Expect = 3e-79 Identities = 141/301 (46%), Positives = 207/301 (68%), Gaps = 4/301 (1%) Query: 2 EYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIF 61 +YF + L GLT GSIY L+A+GYTMVYGII +INFAHG+++M+G F ALIV VL Sbjct: 4 QYFCELLFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMIGAFTALIVAGVLG--I 61 Query: 62 AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQV 121 G P A +L++ +VA++ + + +T+E+VAY+PLR + RL+PLI+AIGMSI L N++ + Sbjct: 62 YGFPEAGILIIAAIVAVIYCAAYGFTLEKVAYKPLRDAPRLSPLISAIGMSIFLQNYVIL 121 Query: 122 TQGPRNKPIPPMVSSVYQFGNIS--VSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179 Q P P +V + I+ ++IIV +A+ + + T +G+A RAT Sbjct: 122 AQTSDFVPFPRLVPDLAILEPIAHITGTSDVLIIVTSAITMVGLTLFIKYTRMGKAMRAT 181 Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239 Q+RKMA LLG++ D+ IS+TF++G++LAA+ G + + G +F GF G+KAFTAAV Sbjct: 182 AQNRKMAMLLGIDADRVISLTFIIGSSLAAIGGVLIASHIGQVNFAIGFIAGIKAFTAAV 241 Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEK 299 LGGIGS+PGA+ GGL++GL ES + Y + Y+D FA+L +LIF+P+GILG+P+ +K Sbjct: 242 LGGIGSIPGAMAGGLVLGLCESFATGYVSSDYEDALAFALLVLILIFRPSGILGKPKTQK 301 Query: 300 V 300 V Sbjct: 302 V 302 Lambda K H 0.329 0.143 0.421 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: 351 Number of extensions: 21 Number of successful extensions: 5 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: 300 Length of database: 302 Length adjustment: 27 Effective length of query: 273 Effective length of database: 275 Effective search space: 75075 Effective search space used: 75075 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 (21.8 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