Align ABC transporter for Lactose, ATPase component (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 248 bits (632), Expect = 2e-70 Identities = 131/286 (45%), Positives = 184/286 (64%), Gaps = 4/286 (1%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 + +V K +G L + V L + GEF +GPSGCGK+TLLRM+AG E + G + ID Sbjct: 15 ITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILID 74 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123 +++V P+KR + MVFQSYA++PHMTV +N+ + L+ VP+AE E RV EA +++L Sbjct: 75 GQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQL 134 Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183 G L RKP QLSGGQRQRVA+ RA+V+ P++ L DEPLS LDA+LR MR E+ L +++ Sbjct: 135 GGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKV 194 Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243 T + VTHDQ EA+ LA + VM G+++QV +P DLY+ P + FVA FIG ++N + Sbjct: 195 GITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIG--QVNLFE 252 Query: 244 GVIEIDE-DQAYARLPDYG-DAKIPVTLQAAAGTAVTIGIRPEHFD 287 GV+ +DE A + PD D + + G V IRPE + Sbjct: 253 GVLAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWAAIRPEKIE 298 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: 331 Number of extensions: 13 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: 381 Length adjustment: 30 Effective length of query: 328 Effective length of database: 351 Effective search space: 115128 Effective search space used: 115128 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