Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 238 bits (608), Expect = 2e-67 Identities = 130/282 (46%), Positives = 172/282 (60%), Gaps = 1/282 (0%) Query: 4 VTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIF 63 V+F+ SY G + V+ NL+I GEFL L+GPSG GK+T+L MLAG E T G I Sbjct: 11 VSFRGIQKSYDG-ESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIL 69 Query: 64 IGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATL 123 + + + +V P RD+ MVFQNYAL+PHMTV EN+ F L + G ++ +I +RV A A + Sbjct: 70 LDGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMV 129 Query: 124 GLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQR 183 L F R P LSGGQ+QRVA+ RA+V PQ+ LMDEPL LD +LR Q + +I L Sbjct: 130 QLEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHE 189 Query: 184 KLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNL 243 +LGVT VYVTHDQ EALTM DR+AV G +QQ+ PR LY++P N FVA F+G Sbjct: 190 RLGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGENNRLP 249 Query: 244 GTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPE 285 + GD+ + + E LA +++ RPE Sbjct: 250 AHLLDRRGDSCTVKLGRGETVEALAVNVGAAGTPVSLSIRPE 291 Lambda K H 0.316 0.135 0.380 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: 349 Number of extensions: 20 Number of successful extensions: 1 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: 376 Length of database: 369 Length adjustment: 30 Effective length of query: 346 Effective length of database: 339 Effective search space: 117294 Effective search space used: 117294 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: 41 (21.6 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