Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_023434296.1 N177_RS20205 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000496075.1:WP_023434296.1 Length = 312 Score = 410 bits (1055), Expect = e-119 Identities = 214/313 (68%), Positives = 252/313 (80%), Gaps = 14/313 (4%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 MEYFVQQL+NGLTLGSIYGL+AIGYTMVYGIIGMINFAHGDIFM+G F ALI + + Sbjct: 1 MEYFVQQLINGLTLGSIYGLIAIGYTMVYGIIGMINFAHGDIFMVGSFIALIAIIAF-GL 59 Query: 61 FAGLPVAVLLLVM---LVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSN 117 AG +AVL+L + L++AM +TS++ WT+ER+AYRPLRGSFRLAPLITAIGMSI L N Sbjct: 60 TAGSSLAVLILALILVLLIAMALTSVYGWTVERLAYRPLRGSFRLAPLITAIGMSIVLQN 119 Query: 118 FIQVTQGPRNKPIPPMVSSVYQFGN----------ISVSLKQIIIIVITAVLLTIFWYIV 167 F+Q+ QG R KP+ P+ S + +++S QI+IIV T VL+T+F I+ Sbjct: 120 FVQIAQGARVKPLQPLFSGGFTLMELEGPTGAVFRVNLSFAQILIIVTTVVLMTVFTLII 179 Query: 168 NRTALGRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDG 227 +T+LGR+QRA EQDRKMAALLGVNVD+TIS+TFVMGAALAAVAG MYL+YYGV F G Sbjct: 180 AKTSLGRSQRACEQDRKMAALLGVNVDRTISLTFVMGAALAAVAGLMYLLYYGVIDFYIG 239 Query: 228 FTPGVKAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFK 287 F GVKAFTAAVLGGIGSLPGA+ GGLLIGLIE+ WSAYF+I YKDVA F+ILA VLIF Sbjct: 240 FIAGVKAFTAAVLGGIGSLPGAMLGGLLIGLIETFWSAYFSIEYKDVAAFSILAIVLIFL 299 Query: 288 PTGILGRPEVEKV 300 P+GILGRPEVEKV Sbjct: 300 PSGILGRPEVEKV 312 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: 426 Number of extensions: 14 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: 300 Length of database: 312 Length adjustment: 27 Effective length of query: 273 Effective length of database: 285 Effective search space: 77805 Effective search space used: 77805 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 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