Align ABC transporter for Lactose, ATPase component (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__BFirm:BPHYT_RS17470 Length = 362 Score = 345 bits (886), Expect = e-100 Identities = 183/322 (56%), Positives = 233/322 (72%), Gaps = 12/322 (3%) Query: 1 MSELQLSDVRKSYGGLE-VIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGD 59 M+ L L V+K+Y G + V+ G+D+D+ GEFVV VGPSGCGKSTLLRM+AGLE IS G Sbjct: 1 MAALTLQGVKKTYDGKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEGS 60 Query: 60 LTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAH 119 ++I +N ++P R IAMVFQ+YALYPHM+V ENMG+AL+ AGV RA+I KRV+ AA Sbjct: 61 ISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAAQ 120 Query: 120 ILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARL 179 ILEL ALL RKP++LSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA LRV MR+EI RL Sbjct: 121 ILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180 Query: 180 HKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKM 239 H +LATT +YVTHDQ+EAMTLA +++VM G EQ+G+P ++Y+ PA +FVA FIGSP M Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPGM 240 Query: 240 NFLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAV------TIGIRPEHFD--EAGP 291 N L+G + +D A+ + G K+P+T A+ G V T+GIRPEH +A Sbjct: 241 NLLEG--RVSDDGAFFEVAGNG-PKLPLTDVASIGREVARGREWTLGIRPEHMSPGQADA 297 Query: 292 AALDLAIDMLEHLGGETFAYAR 313 L +D E LG + A+ R Sbjct: 298 PHATLTVDSCELLGADNLAHGR 319 Lambda K H 0.321 0.139 0.396 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: 386 Number of extensions: 12 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: 358 Length of database: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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