Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate YP_002827025.1 NGR_c25150 ABC transporter substrate-binding protein
Query= uniprot:Q1MDE9 (367 letters) >NCBI__GCF_000018545.1:YP_002827025.1 Length = 372 Score = 334 bits (856), Expect = 3e-96 Identities = 169/353 (47%), Positives = 227/353 (64%), Gaps = 1/353 (0%) Query: 10 LVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKVVLEL 69 L A +AF+ A AD+ +G+ PLTGP AA+G Q++ GA+ A +IN GGI GE++ L L Sbjct: 11 LTAMVAFSGTAWADLLVGVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIKLVL 70 Query: 70 ADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAPDLTK 129 DD +PKQG+S ANK V DG++FVVG SGV+IP S+V AENG+L +TP+AT P T+ Sbjct: 71 GDDVSDPKQGISVANKFVADGVKFVVGHFNSGVSIPASEVYAENGILEITPSATNPQFTE 130 Query: 130 RGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNAGGIT 189 RG+ N RTCGRDDQQ VA Y+ NFKD ++AI++DK YG+GLAD K N G+T Sbjct: 131 RGMWNTFRTCGRDDQQGAVAGAYLAANFKDAKIAIIHDKTPYGQGLADETKKATNEAGLT 190 Query: 190 EVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIGGDGL 249 E + + I GDKDFSAL ++K V VVY+GG H E GL+ RQ+ D AT + GDG+ Sbjct: 191 EALYEGINIGDKDFSALIAKMKEAGVSVVYYGGLHTEAGLIMRQMKDQGLKATFMSGDGI 250 Query: 250 SNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLNAYAAVEVLKA 309 + E +I DA GT+ T A D K+P SK + A EA+TL +YAA++V+ A Sbjct: 251 VSNELASIAGDAVDGTLMTFAPDPRKNPASKELVEKFRAAGFEPEAYTLYSYAALQVI-A 309 Query: 310 GIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWEAGK 362 KA D +AVA A+K TAIG++ Y E GD+T + +Y W+ G+ Sbjct: 310 DAAKAAGGNDPQAVAEAIKAKGPFKTAIGELGYDEKGDITRPDYVMYTWKKGE 362 Lambda K H 0.312 0.131 0.362 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: 436 Number of extensions: 21 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: 367 Length of database: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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