Align L-lactate transporter; SfMCT (characterized)
to candidate AZOBR_RS07945 AZOBR_RS07945 spermidine/putrescine ABC transporter substrate-binding protein
Query= SwissProt::A0LNN5 (412 letters) >FitnessBrowser__azobra:AZOBR_RS07945 Length = 432 Score = 189 bits (479), Expect = 2e-52 Identities = 129/423 (30%), Positives = 195/423 (46%), Gaps = 28/423 (6%) Query: 5 QTTMP---RWVPLLLGLLGSTTCGMLLYAWSVFIKPLNAEFGWSRAEIAMAFAICCLIFG 61 Q+ +P RW+ LL G++ + L Y W++F++P++ + GW RA I +AF I + Sbjct: 7 QSALPVGGRWMQLLAGVICMSMIANLQYGWTLFVEPIDDKHGWGRAAIQVAFTIFIVTET 66 Query: 62 LMTFPAGRLSDKMGPRKVVMTGGVLLAIGFILSGFIQSKYQLYITYGVIAGFGGGMIYLP 121 + G D+ GPR VV+ G VL A + L+ S LY+ I G G G +Y Sbjct: 67 WLVPVEGWFVDRFGPRIVVLFGSVLCAASWALNAVADSLLVLYVA-AAIGGIGAGAVYGT 125 Query: 122 PIATAPKWWPDRRALATGFAVVGLGLGSFL-MGPLATYIIEKPGMGWRYVFWYCGVAMGI 180 + A KW+PDRR LA G G G GS L + P+AT I G+ F G+ G+ Sbjct: 126 CVGNALKWFPDRRGLAAGITAAGFGAGSALTVVPIATMIETS---GYEATFMAFGLGQGL 182 Query: 181 MALIAGAFLEPPPAGWKPAGYTPPAPPAGAAAPKVTRDWTYEEAKGDTKFWLLYLAYFCG 240 + L PP+ P G A P R +T + FW++Y + Sbjct: 183 VVFALAWLLVAPPSA--------PLARGGFATPPAQRQYTPSQMVRTPVFWVMYAMFVMV 234 Query: 241 SFAGLMVIGHLAGFGRD----------AGLTAMAAAGAVSSLAFSNAATRILSGWFVDKI 290 + GLM L +D GLT A A+S N TR GW D I Sbjct: 235 AGGGLMATAQLGPIAQDFGLAHAPVSILGLTLPALTFALSIDRVLNGLTRPFFGWVSDHI 294 Query: 291 GIRVYFAALFALQTAAMIAIFQLGGSVVGLSIVAIVIGWNYGAMFTLFPATCLQFYGPTA 350 G FA++ ++A+ G V ++ ++ + +G +++LFPA C +G Sbjct: 295 GRENTMFIAFAIEAVGIVALSLYGRDPVAFVLLTGLVFFAWGEIYSLFPACCADTFGSKF 354 Query: 351 QGSNYGLLFTACGLAGFAGPWVGGWLKDTTGTYYLPFLCAAALCALGTAI-VFMTKPPEK 409 SN GLL+TA G A P+ + D TG+++ FL AAA+ AL + +F+ +P Sbjct: 355 AASNAGLLYTAKGTAALLIPF-ANIIADATGSWHAVFLLAAAVNALAAVLALFVLRPMRN 413 Query: 410 KHA 412 + A Sbjct: 414 RMA 416 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: 586 Number of extensions: 39 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: 432 Length adjustment: 32 Effective length of query: 380 Effective length of database: 400 Effective search space: 152000 Effective search space used: 152000 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