Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P31134 (377 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 222 bits (566), Expect = 1e-62 Identities = 145/359 (40%), Positives = 206/359 (57%), Gaps = 27/359 (7%) Query: 20 LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79 L I+ L Y G+ + ++LT+ +GEI ALLG SGCGK+TLLR +AG + SAG I ++ Sbjct: 4 LSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAIN 63 Query: 80 GVDLSQ----VPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLG 135 G +S V P R I M+FQ YALFPH+TV NI FG++Q L K + R+ EML Sbjct: 64 GKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQ--LDKQSRSVRLEEMLS 121 Query: 136 LVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDI 195 LV ++ KR PH+LSGGQ+QRV++AR+LA P LLLLDEP +D ++R + LE+ I Sbjct: 122 LVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRAI 181 Query: 196 LERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNV 255 L+ V+ V VTH ++EA A +A+ G+ VQ G PE +Y+ P T Y A+F+G+ N Sbjct: 182 LKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGASN- 240 Query: 256 FEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNF 315 L R E G ++ + G PL D A+ + LRPE++++ E A+G Sbjct: 241 ---YLDVRLEAGQLISTLG-AFPLPQDFKAA---SETGRWLLRPEQLLI--EARADG--- 288 Query: 316 AVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVV 374 GE++ +LG+ Y VRL Q+ + H H G G V L D+ V+ Sbjct: 289 -AGEILERRFLGNGCHYLVRL------GEQVLDIHSH-LGHLACGSRVSLSAAADTPVI 339 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: 293 Number of extensions: 11 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: 377 Length of database: 341 Length adjustment: 29 Effective length of query: 348 Effective length of database: 312 Effective search space: 108576 Effective search space used: 108576 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: 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