Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_038216074.1 Q392_RS27095 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000745855.1:WP_038216074.1 Length = 271 Score = 223 bits (569), Expect = 2e-63 Identities = 115/254 (45%), Positives = 167/254 (65%), Gaps = 5/254 (1%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +L +LS+RFGG+LAVN V V+ +V LIGPNGAGKTTVFN ++ YQPT G+I Sbjct: 6 LLSAHDLSVRFGGVLAVNKVGFEVRRGEVFTLIGPNGAGKTTVFNLISRIYQPTTGSITW 65 Query: 65 DGEP-----IQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFK 119 GE + P H IA G+ RTFQN+ LF+ T + NLLI +H H T F+ +F Sbjct: 66 HGEGGAPVVLTEQPPHAIAALGIARTFQNIELFEHATVLHNLLIGRHTHRRTGFWREVFF 125 Query: 120 TPAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDE 179 TPA R++E EA E AE +D ++L + A L YG ++ +E+AR + T P++L+LDE Sbjct: 126 TPATRRAEIEAREKAEQVIDLLDLQHHRDALAAGLPYGVRKVVELARALCTEPKLLLLDE 185 Query: 180 PAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPE 239 P++GLN +ET D+ I +++E ++VL++EHDM LV +SD ++ +NQG LA GT Sbjct: 186 PSSGLNVEETADMAFWIQDIQQELGISVLMVEHDMTLVSKVSDRVLAMNQGEVLALGTAR 245 Query: 240 QIRDNPEVIKAYLG 253 +++ +P V++AYLG Sbjct: 246 EVQADPRVVEAYLG 259 Lambda K H 0.321 0.138 0.398 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: 184 Number of extensions: 8 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: 255 Length of database: 271 Length adjustment: 25 Effective length of query: 230 Effective length of database: 246 Effective search space: 56580 Effective search space used: 56580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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