Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate WP_002723474.1 RSPH17029_RS19035 ABC transporter permease
Query= CharProtDB::CH_088340 (264 letters) >NCBI__GCF_000015985.1:WP_002723474.1 Length = 267 Score = 173 bits (439), Expect = 3e-48 Identities = 103/265 (38%), Positives = 159/265 (60%), Gaps = 18/265 (6%) Query: 10 FMTAIYAYLYIPIIILIVNSFNSSRFGINWQGFTTKWYSLLMNNDSLLQAAQHSLTMAVF 69 + A+Y +LYIPI I+ + S N+ R GF+ +WY+ ++N +L+A + S T+A+ Sbjct: 4 YAIAVYLFLYIPIGIIALFSLNAGRHATQMTGFSLQWYARALDNPFVLEALKTSFTVALA 63 Query: 70 SATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLL------------V 117 SA AT+ G+L AVAL R R + L++ +M P IV+ I+ L V Sbjct: 64 SALCATVAGTLAAVALQGVRGRLRTLYDAALYMAVMVPGIVIGIATLIALVTVFDLLNPV 123 Query: 118 LFMLLG-----IQLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTI 172 L LLG + LG SL+ +H F + VVV V +RL+G D ++EAA DLGA F Sbjct: 124 LTGLLGDGAPQLGLGKGSLVAAHGLFTMALVVVIVRARLQGMDASLMEAAADLGAPPFRS 183 Query: 173 LRKIILPLAMPAVAAGWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNA 232 +I LP PAV AG++L+FT S DD +++ FV G S LP+ ++S ++ GV+PE+NA Sbjct: 184 FLQITLPQIAPAVLAGFLLAFTFSFDDFIIAFFVAG-SETTLPIYVFSSIRRGVTPEINA 242 Query: 233 LATILLVLSLVMVIASQLIARDKTK 257 + T++L+ SLV++I +Q+I R + + Sbjct: 243 IGTMVLLASLVLLITAQVILRRRAR 267 Lambda K H 0.329 0.141 0.412 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: 190 Number of extensions: 14 Number of successful extensions: 3 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: 264 Length of database: 267 Length adjustment: 25 Effective length of query: 239 Effective length of database: 242 Effective search space: 57838 Effective search space used: 57838 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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