Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate AO353_08575 AO353_08575 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo3_N2E3:AO353_08575 Length = 364 Score = 426 bits (1096), Expect = e-124 Identities = 208/358 (58%), Positives = 269/358 (75%), Gaps = 7/358 (1%) Query: 10 LALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAK 69 + LTLA SV QAA +H+YNWSDYI TL F K TG+K VYDV+DSNE LE K Sbjct: 14 VGLTLAVSV----QAAST--VHIYNWSDYIGQTTLVDFEKATGVKPVYDVFDSNETLEGK 67 Query: 70 LLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAI 129 LLAG +GYDVVVPS+ FL KQIKAG +QKLDKS+LPN+ NL+ L+ LE++DPGN++A+ Sbjct: 68 LLAGHTGYDVVVPSSHFLGKQIKAGAFQKLDKSQLPNYSNLDPALLKRLEMNDPGNQYAV 127 Query: 130 PYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAAL 189 PY+WGT GIGYN DKVKA G + +DSW ++F+PENI+KL CGV+FLDS E+LP L Sbjct: 128 PYLWGTNGIGYNVDKVKAVLGVDK-IDSWAMLFEPENIKKLNSCGVAFLDSADEMLPTVL 186 Query: 190 HYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAK 249 +Y+G ++ NP + + AE L +RPYVTYFHSSKYISDLANGNICVA+G+SGDI+QAK Sbjct: 187 NYMGLNANSTNPDDYQKAEAKLLAVRPYVTYFHSSKYISDLANGNICVAVGFSGDIFQAK 246 Query: 250 SRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVV 309 +RA EA V V Y IPKEG +FDM+AIPKD+ N + A AF+N+++KPE++A+++D V Sbjct: 247 ARAAEAGKGVNVAYAIPKEGGALWFDMLAIPKDSANVKQAHAFINYVLKPEVIAQVSDAV 306 Query: 310 QFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 + N N A L+ ++IR++ +YP + V+ K Y +LP K QR MTRSWTK+KSGK Sbjct: 307 GYANPNPGADKLMEQSIRSNQSVYPPQAVLDKTYVQVELPPKIQRLMTRSWTKVKSGK 364 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: 449 Number of extensions: 12 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: 364 Length adjustment: 30 Effective length of query: 337 Effective length of database: 334 Effective search space: 112558 Effective search space used: 112558 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 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