Align L-lactate transporter; SfMCT (characterized)
to candidate AZOBR_RS07885 AZOBR_RS07885 spermidine/putrescine ABC transporter substrate-binding protein
Query= SwissProt::A0LNN5 (412 letters) >FitnessBrowser__azobra:AZOBR_RS07885 Length = 433 Score = 176 bits (445), Expect = 2e-48 Identities = 122/409 (29%), Positives = 188/409 (45%), Gaps = 24/409 (5%) Query: 10 RWVPLLLGLLGSTTCGMLLYAWSVFIKPLNAEFGWSRAEIAMAFAICCLIFGLMTFPAGR 69 RW L++G++ + L Y W++F++P++ + GW RA I +AF I ++ + G Sbjct: 16 RWFQLVIGVICMSMIANLQYGWTLFVEPIDQKHGWGRAAIQVAFTIFVVMETWLVPVEGW 75 Query: 70 LSDKMGPRKVVMTGGVLLAIGFILSGFIQSKYQLYITYGVIAGFGGGMIYLPPIATAPKW 129 DK GPR VV+ GGVL A + ++ S LY+ + G G G +Y + A KW Sbjct: 76 FVDKFGPRIVVLIGGVLCAAAWAVNSVADSLAMLYLG-AALGGIGAGGVYGTCVGNALKW 134 Query: 130 WPDRRALATGFAVVGLGLGSFL-MGPLATYIIEKPGMGWRYVFWYCGVAMGIMALIAGAF 188 +PDRR LA G G G GS L + P+A I G+ F G+ G + L F Sbjct: 135 FPDRRGLAAGLTAAGFGAGSALTVVPIANMI---HSSGYEATFMTFGIGQGAVILALAWF 191 Query: 189 LEPPPAGWKPAGYTPPAPPAGAAAPKVTRDWTYEEAKGDTKFWLLYLAYFCGSFAGLMVI 248 L P G P +A + +T + FW++Y + + GLM Sbjct: 192 LASPKKGQVP-------EVTRSAVSQTRESYTPVQMLKTPVFWVMYAMFVMVAAGGLMAT 244 Query: 249 GHLAGFGRD----------AGLTAMAAAGAVSSLAFSNAATRILSGWFVDKIGIRVYFAA 298 L +D GLT A A+S N TR GW D IG Sbjct: 245 AQLGPIAKDFHLDGVPVSIMGLTLPALTFALSIDRVLNGVTRPFFGWVSDHIGRENTMFI 304 Query: 299 LFALQTAAMIAIFQLGGSVVGLSIVAIVIGWNYGAMFTLFPATCLQFYGPTAQGSNYGLL 358 FAL+ ++A+ Q G + V I+ ++ + +G +++LFPA C +G +N GLL Sbjct: 305 AFALECVGILALNQWGHNPVAFVILTGLVFFAWGEIYSLFPALCGDSFGSKFATTNAGLL 364 Query: 359 FTACGLAGFAGPWVGGWLKDTTGTYYLPFLCAAALCALGTAI-VFMTKP 406 +TA G A P+ + +TG++ F AAA+ + + +F+ KP Sbjct: 365 YTAKGTASLVVPFANVAVA-STGSWQAVFFFAAAVNGIAALLAIFVLKP 412 Lambda K H 0.327 0.142 0.475 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: 563 Number of extensions: 33 Number of successful extensions: 6 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: 412 Length of database: 433 Length adjustment: 32 Effective length of query: 380 Effective length of database: 401 Effective search space: 152380 Effective search space used: 152380 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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