Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate SMc01633 SMc01633 ABC transporter permease
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__Smeli:SMc01633 Length = 288 Score = 180 bits (456), Expect = 4e-50 Identities = 98/264 (37%), Positives = 157/264 (59%), Gaps = 6/264 (2%) Query: 1 MIVTIVGWLVLFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLLDPLYFEVLLHSLN 60 +I WL +F+ LP + ++ +F R + FT + L P ++L Sbjct: 16 LIAPAAVWLTVFLVLPFIAMLVFAFGERAPEGGYQPAFTFAQFANL--PTRAAAFWNTLM 73 Query: 61 MALIATLACLVLGYPFAWFLA-KLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGY 119 +A L CLV+ YP A++LA K + R +L+ L++VPFWT+ L+R Y L ++G Sbjct: 74 LAPAGALLCLVVAYPVAYYLAVKANPRYRLILVSLVVVPFWTSLLVRTYAWMYILGSRGI 133 Query: 120 LNEFLLWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGA 179 N L +G+ D +R++ TP AV++G+VY LP M+MP+Y S+EKLD+ LLEA+ DLG Sbjct: 134 PN-LLSMIGIED--VRMLNTPGAVLLGIVYGYLPLMIMPIYVSLEKLDRRLLEASADLGG 190 Query: 180 SKLQTFIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRD 239 + TF+ + +PL++PG++ G LV + +G + + L+GG K IGN + FL R+ Sbjct: 191 KPVSTFLGVTLPLSLPGVMTGVALVTILLLGEYLIPQLLGGGKVFFIGNALVDLFLQSRN 250 Query: 240 WPFGAATSITLTIVMGLMLLVYWR 263 WPFG+A ++TL V+ ++L+V R Sbjct: 251 WPFGSAIAVTLVAVVVVVLMVAMR 274 Lambda K H 0.333 0.148 0.456 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: 281 Number of extensions: 12 Number of successful extensions: 4 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: 275 Length of database: 288 Length adjustment: 26 Effective length of query: 249 Effective length of database: 262 Effective search space: 65238 Effective search space used: 65238 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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