Align Monocarboxylic acid transporter (characterized)
to candidate PP_2797 PP_2797 acetate permease
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__Putida:PP_2797 Length = 552 Score = 385 bits (988), Expect = e-111 Identities = 232/571 (40%), Positives = 332/571 (58%), Gaps = 49/571 (8%) Query: 1 MNSTILLAQDAVSEGVGNPIL--NISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFS 58 ++S +LLA ++ G P+ I +F+VF++ T+ + + T +TDFY+ G Sbjct: 11 LHSGLLLASPSLDAGQRQPLNLHAIGMFMVFVLFTLCITWWAARRTRSTTDFYSAGGGIQ 70 Query: 59 GTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRF 118 G QNGLA+AGDY+SA++ LGI I +G DG++Y I FF W V LLL+ E LRN+GRF Sbjct: 71 GWQNGLALAGDYMSASTLLGITALIYTSGMDGYIYLIAFFAGWPVLLLLMTERLRNLGRF 130 Query: 119 TMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVL--LDIHEFKWQAVVV 176 T AD+ S+RL Q VR AA G+L V FYL+AQM GAG L+ +L LD H + V Sbjct: 131 TFADITSYRLDQGKVRTMAAIGSLTVVCFYLVAQMVGAGQLIRLLFGLDYH------IAV 184 Query: 177 GIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKH 236 IVG +M+ YV GGM TT+VQ+IKA LL+ G +++ L + L++ A++ H Sbjct: 185 VIVGALMMLYVTFGGMVATTWVQIIKAFLLLVGGSLVLFLAMREFDFSYDALVSKAMDTH 244 Query: 237 AASDYAATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTA 296 A + ++L P G+ L L +SL+L L GTAGLPH+LMRF+TV A Sbjct: 245 ALGE----------RLLAP----GSLLADPLTALSLSLGLVFGTAGLPHILMRFFTVSDA 290 Query: 297 KEARKSVTWAIVLIGAFYLMTLVLGYGAAALV--------GPDRVIAAPGAANAAAPLLA 348 +EARKSV +A IG F+ + +LG + +V G + G N LA Sbjct: 291 REARKSVLYATGFIGYFFNVIFLLGLASIVIVSQQPKFFEGGEVGGKLLGGGNMVVMHLA 350 Query: 349 FELGGSIFMALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRI 408 +GG++ + +SAV FAT+LAVV+GLA+ ++A+ HD+Y VI G ++EA+++RV+++ Sbjct: 351 QAVGGNLLLGFLSAVTFATILAVVSGLALAGASAIAHDLYARVIMKGAASEAQELRVTKL 410 Query: 409 TVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYT 468 + +GL++I LGIL NVAF+VALAF +AASAN P + S++W T GA+AA Y Sbjct: 411 ATLSLGLVAIALGILFENINVAFMVALAFGIAASANFPVLFLSMFWSGLTTRGALAAGYV 470 Query: 469 GLISALLLIFLSPAVSGNDSAMVPGADWA--IFPLKNPGLVSIPLAFIAGWIGTLVGKPD 526 GL+SA+ + S V V +A +FP P L S+PLAF+ + V + D Sbjct: 471 GLLSAMGFVVFSKLV------WVDVLHFAEPLFPYTQPALFSMPLAFLVAY---AVSRMD 521 Query: 527 NMDDLAAEME------VRSLTGVGVEKAVDH 551 AE VR TG+G AVDH Sbjct: 522 RTARAKAERAAFADQFVRGQTGLGASGAVDH 552 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: 644 Number of extensions: 31 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: 552 Length adjustment: 36 Effective length of query: 515 Effective length of database: 516 Effective search space: 265740 Effective search space used: 265740 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: 53 (25.0 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