Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= TCDB::P31134 (377 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 267 bits (682), Expect = 4e-76 Identities = 147/322 (45%), Positives = 208/322 (64%), Gaps = 11/322 (3%) Query: 19 LLEIRNLTKSYDGQHA-VDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 L+ R + KSYDG+ V D++L I +GE LLG SG GK+T L MLAGFE P+AG+I+ Sbjct: 10 LVSFRGIQKSYDGESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIL 69 Query: 78 LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137 LDG ++ VPP+ R + M+FQ+YALFPHMTV +N+AF L + K +I RV L +V Sbjct: 70 LDGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMV 129 Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197 ++ F R P QLSGGQ+QRVALAR+L P+L+L+DEP+GALDK+LR++MQ+E+ + E Sbjct: 130 QLEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHE 189 Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFE 257 R+GVT V VTHDQ EA+TM+ R+A+ ++G+ QI +P +YE P + A F+G N Sbjct: 190 RLGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGENNRLP 249 Query: 258 GVLKERQEDG--LVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNF 315 L +R+ D + L V L V+ A+ PV +++RPE+++L AN N Sbjct: 250 AHLLDRRGDSCTVKLGRGETVEALAVNVGAA---GTPVSLSIRPERVLL-NGASANCPNR 305 Query: 316 AVGEVIHIAYLGDLSVYHVRLK 337 G V YLGD H+R++ Sbjct: 306 FTGRVAEFIYLGD----HIRIR 323 Lambda K H 0.321 0.137 0.400 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: 364 Number of extensions: 15 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: 377 Length of database: 369 Length adjustment: 30 Effective length of query: 347 Effective length of database: 339 Effective search space: 117633 Effective search space used: 117633 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