Align Monocarboxylic acid transporter (characterized)
to candidate PP_3272 PP_3272 acetate permease
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__Putida:PP_3272 Length = 520 Score = 434 bits (1117), Expect = e-126 Identities = 242/537 (45%), Positives = 334/537 (62%), Gaps = 30/537 (5%) Query: 23 ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 IS+F+VF+ T+ V T ++DFYT G +G QNGLAIAGD +SAASFLGI Sbjct: 6 ISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLGISAM 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 + +NGYDG LY++G W + L L+AE LRN+G++T ADV+S+RL Q PVR+ +A GTL Sbjct: 66 MFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSAFGTL 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 V L YL+AQM GAG L+ +L I V +VG++M++YV GGM TT+VQ+IK Sbjct: 126 VVALMYLVAQMVGAGKLIELLFGIS----YLYAVMLVGVLMVSYVTFGGMLATTWVQIIK 181 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262 AV+L+ G + M + + AV HA KG I+ P G Sbjct: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHA-------KG---QAIMAP----GGL 227 Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322 L+ +D ISL L + GTAGLPH+LMRF+TV AKEARKSV +A IG FYL+ +V+G+ Sbjct: 228 LSNPVDAISLGLGMMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVVGF 287 Query: 323 GAAALVGP-----DRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377 GA +VG D A G N A LA +GG++F+ ISAVAFAT+LAVVAGLA+ Sbjct: 288 GAIVMVGTEPSYRDATGAIIGGGNMVAVHLAQAVGGNLFLGFISAVAFATILAVVAGLAL 347 Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437 + ++AV HD+Y V+R G++TE E++RVSRI ++IGL++++LG++ +QN+AFL L Sbjct: 348 SGASAVSHDLYACVMRKGKATEQEEMRVSRIATLLIGLLAVILGLMFESQNIAFLSGLVL 407 Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWA 497 AVAAS N P +L S++WK T GAV GL+SA+LL+ L PAV N V + A Sbjct: 408 AVAASVNFPVLLLSMFWKGLTTRGAVCGSMAGLVSAVLLVVLGPAVWVN----VLHNETA 463 Query: 498 IFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE---MEVRSLTGVGVEKAVDH 551 +FP NP L S+ LAF++ W+ ++ + + +RS+TG+G A H Sbjct: 464 LFPYSNPALFSMSLAFLSAWVFSVTDTSERAVEERGRYLGQFIRSMTGIGAAGASKH 520 Lambda K H 0.324 0.138 0.393 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: 667 Number of extensions: 30 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: 551 Length of database: 520 Length adjustment: 35 Effective length of query: 516 Effective length of database: 485 Effective search space: 250260 Effective search space used: 250260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.6 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