Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_043828072.1 RSPH17029_RS08325 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_000015985.1:WP_043828072.1 Length = 365 Score = 279 bits (714), Expect = 8e-80 Identities = 151/367 (41%), Positives = 224/367 (61%), Gaps = 9/367 (2%) Query: 12 TRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQP 71 T A ++E R++ K Y HA+ +S TI GE F+LLG SGCGK+TLLR +AGFE+ Sbjct: 2 TVAAKPTMIEFRDVHKYYGDYHALRGISATIRAGEFFSLLGPSGCGKTTLLRTIAGFEEI 61 Query: 72 SAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVN 131 S+G +++DG D VP RP NM+FQSYA+FPH+TV +N+ FGL++ L K E RV Sbjct: 62 SSGVVLIDGKDTKGVPANKRPTNMVFQSYAIFPHLTVAENVGFGLRRANLSKEETTRRVA 121 Query: 132 EMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLE 191 E L +V ++ + R H LSGGQRQRVALAR+L +PK+LLLDEP+ ALDKK+R++MQ+E Sbjct: 122 EALEMVGLRGYGARAAHALSGGQRQRVALARALILKPKVLLLDEPLSALDKKMREQMQVE 181 Query: 192 VVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIG 251 ++ + +VG+T ++VTHDQEEA+ M+ RIA+M G+ Q+ +PE +Y PT+R A+FIG Sbjct: 182 LIKLQRQVGITFILVTHDQEEALVMSDRIAVMFEGEIAQLADPETLYRRPTSRKVADFIG 241 Query: 252 SVNVFEGVLKERQEDGLVLDSPG----LVHPLKVDADASVVDNVPVHVALRPEKIMLCEE 307 ++N + G+ +++ G L+ P++ AS V V RPE + E Sbjct: 242 TMNFLPARILSETGQGIEVEAQGLGRMLLDPMQAPGAAS---GTGVTVGFRPETATILFE 298 Query: 308 PPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCW 367 A+G + + Y GD++ Y +RL G +L + + + G R+ W Sbjct: 299 -GQKADREAMGTIEEVVYYGDMTYYDIRL-DGTEAPIRLSMRNVFGRAVLEIGARARVAW 356 Query: 368 EVDSCVV 374 + V+ Sbjct: 357 SPGALVL 363 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: 343 Number of extensions: 9 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: 365 Length adjustment: 30 Effective length of query: 347 Effective length of database: 335 Effective search space: 116245 Effective search space used: 116245 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 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