Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_162602315.1 DNK54_RS05345 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_003194585.1:WP_162602315.1 Length = 462 Score = 143 bits (361), Expect = 7e-39 Identities = 94/296 (31%), Positives = 155/296 (52%), Gaps = 7/296 (2%) Query: 5 VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI-FAG 63 V L GL SI + ++G MV+G G+ NFAHG++ G A + + SI AG Sbjct: 167 VNLLATGLVYSSILAMASLGLNMVFGTTGLTNFAHGELMTFGALIAFAIDSLPGSISIAG 226 Query: 64 LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLR--GSFRLAPLITAIGMSITLSNFIQV 121 +V+ V +V L + ++ W ++ + PLR G+ +A +I +IG+SI L N Q Sbjct: 227 HDFSVV--VACLVGFLASGIFGWLNDKGLWLPLRRRGTGVIAMMIVSIGLSIFLRNLYQY 284 Query: 122 TQGPRNKPIPPMVS-SVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 G +N + S FG + V+ QI + +++ +L + ++ T LG+A RA Sbjct: 285 FAGGQNHNYSQYTNISPMTFGPLQVTSLQITVFIVSVTVLVVACLLLQYTRLGKATRAVA 344 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240 + +AA G+NV++ I+ +V GAALA ++G + + G ++ G+ + F A L Sbjct: 345 DNPALAASSGINVERVINRVWVFGAALAGLSGALLGVTQGF-NYQVGYKALLMIFAAVCL 403 Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPE 296 GG+G++ GA+ G +IG+ L + K V +L VL+ +P GILGR E Sbjct: 404 GGLGTVWGAIAGAFVIGIFIELSTLVVPDELKYVGALGVLIVVLMVRPQGILGRRE 459 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: 18 Number of successful extensions: 4 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: 462 Length adjustment: 30 Effective length of query: 270 Effective length of database: 432 Effective search space: 116640 Effective search space used: 116640 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: 49 (23.5 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