Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate WP_110804792.1 C8J30_RS05885 amino acid ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc02118 (341 letters) >NCBI__GCF_003217355.1:WP_110804792.1 Length = 338 Score = 385 bits (990), Expect = e-112 Identities = 195/330 (59%), Positives = 239/330 (72%), Gaps = 3/330 (0%) Query: 13 AVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFDVDYCKAIAAAIF 72 A+V + AASA+TLDDVKA+G + CGVN GL GF APDA+GN+ GFDV CKA+AAA+ Sbjct: 11 ALVALVAGAASASTLDDVKARGQLICGVNPGLTGFGAPDANGNYQGFDVAACKAVAAAVL 70 Query: 73 GDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRPVNYYDGQGFMVR 132 GD KV+Y L+ + RF AL SGEVD+LARN+TW+ RDT L +F VNYYDGQGFMV Sbjct: 71 GDPMKVQYKALTGETRFTALASGEVDMLARNSTWTFGRDTELALDFVAVNYYDGQGFMVN 130 Query: 133 KELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLEEVNAAYDAGRCD 192 K L V SA EL GA VCVQTGTTTE+NLADYFK+NN+ Y PV E + AG CD Sbjct: 131 KSLGVSSAKELDGATVCVQTGTTTEMNLADYFKSNNMTYTPVNIADDAEGQQKFLAGACD 190 Query: 193 VYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDIVSWVHYALVQAE 252 YTTD SGL + R T+ D ++LPEIISKEPLA AVR GD+ W DIV W YALV AE Sbjct: 191 SYTTDASGLAASRATMPNAADIVILPEIISKEPLALAVRHGDNNWGDIVRWSFYALVAAE 250 Query: 253 EFGVTQANLEEMKKST-NPDVQRFLGVEADSKIGTDLGLTNEWAVNIVKAVGNYGEVFDR 311 E+G+T+ANLEE+ ST NP+++R LG+E D +G +GL N++A + A GNYGE+F+ Sbjct: 251 EYGITKANLEEVAASTQNPEIRRLLGLEGD--MGKKIGLDNDFAKRAIMASGNYGEIFEA 308 Query: 312 NIGAGSPLKIERGLNALWNKGGLQYAPPVR 341 NIGA + + + RGLNA W +GGL YAPP R Sbjct: 309 NIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 Lambda K H 0.317 0.134 0.399 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: 422 Number of extensions: 17 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: 341 Length of database: 338 Length adjustment: 28 Effective length of query: 313 Effective length of database: 310 Effective search space: 97030 Effective search space used: 97030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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