Align D-mannose and D-mannitol transporter (characterized)
to candidate PfGW456L13_3476 D-glucarate permease
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3476 Length = 467 Score = 209 bits (532), Expect = 1e-58 Identities = 134/420 (31%), Positives = 211/420 (50%), Gaps = 27/420 (6%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R LI+ ++ + ++ DR+ALSVA + K+ G+S+ EMG +FS+F Y F GW Sbjct: 38 RFLILALITIVLALSTGDRAALSVAGTDMSKELGISSVEMGYLFSAFSWAYVIFLIPSGW 97 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFASLVL-----IRILFGMGEGPLSVTTSKM 120 DR G+K +++LA+V+WS F+ + + V F +V+ +R L G E P+ + ++ Sbjct: 98 LTDRIGSKLSMMLAVVIWSCFTVMMGM-VHFIGMVVPLLLALRFLLGAAESPVGPASGRI 156 Query: 121 VNNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWF 180 + W+ R A S L A+ PV+G++ TYGW+ FII+ IGLV A+W+ Sbjct: 157 IAAWFPSSERGIAGAIFNSAQYLSLAVFTPVMGWLCYTYGWEYVFIIMGAIGLVIGAIWW 216 Query: 181 KFVK---ERPE-----------GEGAEDI--LRAEGQGELAAQPVFPLRFYLKQPTVLFT 224 KF + P+ G+G D+ L+++ + + + ++ Sbjct: 217 KFYYLPIDHPKMNSEELEYIRAGDGLVDLESLKSKAANTGKGMKLGEIGQLFRSRMLVGI 276 Query: 225 SLAFFSYNYTLFFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFK 284 LA + +FF+TWFP YL G ++ IP + G +G GFISD + K Sbjct: 277 FLAQYCITSITWFFMTWFPIYLVKERGFDILQAGFIAAIPALCGLVGGVSSGFISDLILK 336 Query: 285 KTGRMMFSRKVVLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQD 344 KTG + +RK + LL A I C + V+L++LA FF G++ W ++ D Sbjct: 337 KTGSLSIARKTPITIGLLLSASIILC-NYAESAAVVVVLMSLA-FFGKGFGSMGWTVVAD 394 Query: 345 TVPAARVGGVSGFMHFLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARY 404 T P +G G + NT+GIV P + G+++Q TGSF A L G G V VA Y Sbjct: 395 TAPKELIGTTGGVFNAFGNTAGIVTPVVIGYILQTTGSFDGALLYVG---AHGLVAVASY 451 Lambda K H 0.329 0.142 0.439 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: 622 Number of extensions: 37 Number of successful extensions: 4 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: 430 Length of database: 467 Length adjustment: 33 Effective length of query: 397 Effective length of database: 434 Effective search space: 172298 Effective search space used: 172298 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 (21.8 bits) S2: 51 (24.3 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