Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 219 bits (557), Expect = 1e-61 Identities = 130/348 (37%), Positives = 193/348 (55%), Gaps = 9/348 (2%) Query: 2 ADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTL 61 +D+ C+ L + + V H + L + G F +LGPSGCGK+T+LR++AG + G + Sbjct: 3 SDLFCEGLVRRFGSNAAVDH-VSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDI 61 Query: 62 RIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAAL 121 I G +ND+P R V MVFQ+ AL+P M+V DNIA+GL+R K P E +R+ V Sbjct: 62 HIRGERMNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQ 121 Query: 122 LNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLH 181 + L L R P+ +SGGQ+QR A+AR ++ P++ L DEPL LD KLR Q++ ++K L Sbjct: 122 VGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQ 181 Query: 182 QRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMN 241 ++ TT VY+THDQ EAM ++D+V +M+DGR Q P ELYR P F AGF+G N Sbjct: 182 KQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGD--NN 239 Query: 242 FLSGTVQRQDGQLFIETAHQRWALTGERFS-RLRHAMAVKLAVRPDHVRIAGEREPAASL 300 LSG + L + G S L+ +L +RP+ + ++G+ Sbjct: 240 RLSGELVSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFS 299 Query: 301 TCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALD 348 + V GA++ + Q + A RLPQ G+ L++D Sbjct: 300 SMQAKVRTTLFDGANSRVEAETCGQPVYA-----RLPQDGSAPRLSVD 342 Lambda K H 0.321 0.137 0.403 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: 379 Number of extensions: 16 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: 406 Length of database: 362 Length adjustment: 30 Effective length of query: 376 Effective length of database: 332 Effective search space: 124832 Effective search space used: 124832 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: 50 (23.9 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