Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 341 bits (874), Expect = 2e-98 Identities = 181/367 (49%), Positives = 241/367 (65%), Gaps = 9/367 (2%) Query: 18 PLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 P++ N+TK + AVD+VSLT+ +GE FALLG SGCGK+TLLRMLAGFE P+ G+I+ Sbjct: 13 PIITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRIL 72 Query: 78 LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137 +DG D+S VPP RP+NM+FQSYA+FPHMTV N+A+GLK D +PKAE +RV E L LV Sbjct: 73 IDGQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELV 132 Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197 + RKP QLSGGQRQRVALAR+L KRP++LLLDEP+ ALD KLR++M+ E+ + E Sbjct: 133 QLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQE 192 Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFE 257 +VG+T +MVTHDQ+EA+ +A R A+M++G Q+ P ++YE P +R+ A+FIG VN+FE Sbjct: 193 KVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQVNLFE 252 Query: 258 GVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIML---CEEPPAN--- 311 GVL + V+ SP L + +D + V A+RPEKI L ++ P N Sbjct: 253 GVLAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWAAIRPEKIELHKKADDTPPNLGD 312 Query: 312 ---GCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWE 368 G N G + H AYLG S Y V + G+ + Q N R + G+ V LCW Sbjct: 313 APKGTNAVEGVIKHEAYLGGSSTYEVEIAGGRRVKVQRSNLTRWDQEDFKLGETVWLCWH 372 Query: 369 VDSCVVL 375 S VL Sbjct: 373 ACSPAVL 379 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: 389 Number of extensions: 14 Number of successful extensions: 2 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: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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