Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate WP_057507763.1 ABB28_RS05955 polyamine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >NCBI__GCF_001431535.1:WP_057507763.1 Length = 370 Score = 398 bits (1022), Expect = e-115 Identities = 190/358 (53%), Positives = 259/358 (72%), Gaps = 1/358 (0%) Query: 11 ALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKL 70 AL A G A D KVL+VYN+SDYIA DT+ F K++GIKV YDV+DS+E++E KL Sbjct: 13 ALLAACGGGGNGAAQDGKVLNVYNYSDYIAEDTIPNFEKQSGIKVTYDVFDSDEMVETKL 72 Query: 71 LAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIP 130 LAG SGYDVVVP+ +F +QI+AGV+ LDK+K+PN L+ +M + DPGN++ +P Sbjct: 73 LAGNSGYDVVVPTLNFFGRQIQAGVFLPLDKAKIPNLAKLDPKVMERIATQDPGNKYGVP 132 Query: 131 YMWGTIGIGYNPDKVKAAFGDNAPV-DSWDLVFKPENIQKLKQCGVSFLDSPTEILPAAL 189 YM GT GIGYN D +K FG +A + +SWDLVFKPENI K+K CGV+ LD+P +++P A+ Sbjct: 133 YMIGTTGIGYNVDMLKERFGGSADIANSWDLVFKPENIAKMKDCGVTLLDTPADMIPVAM 192 Query: 190 HYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAK 249 HYLG P ++NP +++ A EL IRPYV FHSS+Y+ LANG C+ +G+SGDI QA+ Sbjct: 193 HYLGLDPHSNNPADIQKAAELLKSIRPYVQNFHSSQYVGSLANGGTCLVVGWSGDIIQAR 252 Query: 250 SRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVV 309 RAEEA N V V Y+IP+EGA +FDM+AIPKDA+N E A F+N+L++P++ A T+ + Sbjct: 253 DRAEEAANGVHVAYSIPREGAPQWFDMLAIPKDAKNPEAAYQFINYLLEPKVAAANTNFI 312 Query: 310 QFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 + N + ATPLV EAIRNDP IYP +V +K++T+ +T + TR WT+IK+G+ Sbjct: 313 HYGNPVSEATPLVDEAIRNDPTIYPPADVAEKMFTYSINTPETDKLYTRLWTEIKTGR 370 Lambda K H 0.315 0.133 0.390 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: 450 Number of extensions: 20 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: 367 Length of database: 370 Length adjustment: 30 Effective length of query: 337 Effective length of database: 340 Effective search space: 114580 Effective search space used: 114580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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