Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 241 bits (616), Expect = 2e-68 Identities = 145/343 (42%), Positives = 201/343 (58%), Gaps = 7/343 (2%) Query: 6 IEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDIM 65 IE ++V+K + +VL+DIN ++++G+F L+G SG GKST+L +IAGL T+GD Sbjct: 4 IELRDVAKRY--GAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDFE 61 Query: 66 LDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEVLKMV 125 +DG R+ND+ RD+ VFQSYAL+PHM+V N+ F + +RK +E RVA + + Sbjct: 62 IDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAETL 121 Query: 126 QLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELRELQQ 185 L R + LSGGQRQRVA+ RAII PR L DEPLS LD LR +M+ E+ L + Sbjct: 122 GLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLHK 181 Query: 186 RLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGE--SNI 243 +LG T ++VTHDQ EAL ++D I V+N G+I Q G+P+++Y+ P N FVA FIG NI Sbjct: 182 QLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMNI 241 Query: 244 LPGTMIEDYLVEFNGKRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEGKLQVKVDTQLFR 303 LP + ++ NG +D VE+ IRPE L + P EG L D Sbjct: 242 LPVSGAASGVMATNGMML-TLDHMHDTAAAVELGIRPEHLDVVEPGEGHLIAVADVVERL 300 Query: 304 GVHYEIIA-YDELGNEWM-IHSTRKAIVGEEIGLDFEPEDIHI 344 G I A D LG + H GE +GL + ++ HI Sbjct: 301 GSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHI 343 Lambda K H 0.318 0.138 0.386 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: 317 Number of extensions: 14 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: 385 Length of database: 355 Length adjustment: 30 Effective length of query: 355 Effective length of database: 325 Effective search space: 115375 Effective search space used: 115375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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