Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 360 bits (925), Expect = e-104 Identities = 197/369 (53%), Positives = 253/369 (68%), Gaps = 16/369 (4%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 L+++N+ K+YG + LK+I + I+ G+FL+LVGPSGCGKSTL+NCIAGLE I+GG+I Sbjct: 5 LDIKNLYKSYGT--TEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSIN 62 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + D++ +SPKDRDIAMVFQSYALYPTM+V NI FG+K+R + A D ++A+V++ L Sbjct: 63 IGGKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQL 122 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 QIE LL+R+PGQLSGGQ+QRVAMGRAL R PK++LFDEPLSNLDAKLRVEMRTE+K +H Sbjct: 123 QIEPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHH 182 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 L + VYVTHDQIEAMTL K+ VMK G+IQQ G+P +IYN PANLFVA F+GSP MN Sbjct: 183 NLGASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNL 242 Query: 244 IPLRLQRKD--GRLLALLDSGQARCELPLGMQDAGLED--REVILGIRPEQIILANGEAN 299 IP + R D R+ SG+ P+ + D D +VILG+RPE I A+ + Sbjct: 243 IPAKAHRADEGTRIEITRKSGE-----PIVLTDTKNRDLPEDVILGVRPEDI--ADPDLR 295 Query: 300 GLPTIRAE---VQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLL 356 G +A + + EP G DT + L V RL + G+ L FD KV Sbjct: 296 GAEAAQAAECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKRLSFDLGKVSY 355 Query: 357 FDAKTGERL 365 F +TG RL Sbjct: 356 FAPETGLRL 364 Lambda K H 0.319 0.138 0.393 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: 427 Number of extensions: 12 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: 386 Length of database: 365 Length adjustment: 30 Effective length of query: 356 Effective length of database: 335 Effective search space: 119260 Effective search space used: 119260 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 (21.7 bits) S2: 50 (23.9 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