Align ABC transporter for Lactose, ATPase component (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 226 bits (577), Expect = 6e-64 Identities = 133/332 (40%), Positives = 193/332 (58%), Gaps = 22/332 (6%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 L++ V K + + + V L+I GE +G SG GKSTLLRM+AG E+ + G + +D Sbjct: 21 LKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLD 80 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123 + D+ P +R I M+FQSYAL+PHMTV +N+ F L+ +P+AEIE+RV E ++ + Sbjct: 81 GQDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHM 140 Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183 RKP QLSGGQRQRVA+ R++ + PK+ L DEP+ LD +LR M++E+ + + + Sbjct: 141 EPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAV 200 Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243 T V VTHDQ EAMT+A++I +M G + Q GSP+D+Y+ PAN VA FIGS +N + Sbjct: 201 GVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGS--VNLFE 258 Query: 244 G-VIEIDEDQAYARLPDYGDAKIPVTLQAAAG-------TAVTIGIRPE--HFDEAGPAA 293 G ++E + D + A IP G T V + IRPE H P Sbjct: 259 GDIVEDEVDHVVINV-----ANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHISREQPED 313 Query: 294 LDL----AIDMLEHLGGETFAYARHHGNGELI 321 ++ + +LGG + Y R NG+LI Sbjct: 314 ARNWCAGKVEDIAYLGGISVYYIR-LCNGQLI 344 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: 321 Number of extensions: 11 Number of successful extensions: 1 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: 378 Length adjustment: 30 Effective length of query: 328 Effective length of database: 348 Effective search space: 114144 Effective search space used: 114144 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