Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 430 bits (1105), Expect = e-125 Identities = 225/358 (62%), Positives = 273/358 (76%), Gaps = 2/358 (0%) Query: 19 LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78 LL IR ++KS+DG AVD+V+L I+KGEIFALLG SG GKSTLLRMLAGFE P+AG IML Sbjct: 14 LLSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIML 73 Query: 79 DGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVH 138 DG D++ +PP+LRP NMMFQSYALFPHMTVEQNIA GLKQDKLPK+EI RV ML LV Sbjct: 74 DGQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVK 133 Query: 139 MQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILER 198 M+ +A+RKP QLSGGQ+QRVALARSLAKRPKLLLLDEPMGALDKKLR MQLE+V+ILE Sbjct: 134 MEPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILEN 193 Query: 199 VGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEG 258 VG TC+MVTHDQEEAMTMA RIAIM +G+ QIG P +IYE P +R +AEFIGSVN+FE Sbjct: 194 VGATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGSVNIFEA 253 Query: 259 VLKERQEDGLVLDSPGLVHPLKVDADASV-VDNVPVHVALRPEKIMLCEEPPANGCNFAV 317 ++E + D + L S L P+ +D + ++ VALRPEKI L + P N++ Sbjct: 254 HIREDEADSVTLTSDLLDAPVFIDRGVTTPAESTATLVALRPEKIYLTPDKPDGENNWSC 313 Query: 318 GEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVL 375 G V +IAYLGD++ Y+V+L SG+ + A + N R R PTWGD V + WE S ++L Sbjct: 314 GTVDNIAYLGDITSYYVKLASGKRVQATMANVER-RGERPTWGDRVFVSWEASSPILL 370 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: 403 Number of extensions: 7 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: 372 Length adjustment: 30 Effective length of query: 347 Effective length of database: 342 Effective search space: 118674 Effective search space used: 118674 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