Align Proline-specific permease (ProY) (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP
Query= TCDB::P37460 (456 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Length = 473 Score = 365 bits (936), Expect = e-105 Identities = 195/460 (42%), Positives = 277/460 (60%), Gaps = 12/460 (2%) Query: 4 NNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALG 63 + +LKRGL RHI+ +ALG AIGTGLF GSA +K AGPS++L Y I G A++IMR LG Sbjct: 8 SGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLG 67 Query: 64 EMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPH 123 EM V P A SFS +A + G AG+++GW ++V ++++TA G Y+ W P +P Sbjct: 68 EMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPT 127 Query: 124 WIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTG 183 W+ ++I INL +VKVFGE EFWF+ KV I+ MI G ++V G+GG Sbjct: 128 WVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLV--SGDGGPQAS 185 Query: 184 IHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRI 243 + NLW +GGFF NG G++M++ ++MF++GG+E++G TA EA P+ IP+AIN V RI Sbjct: 186 VTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRI 245 Query: 244 LVFYVGTLFVIMSIYPWNQVGT---------NGSPFVLTFQHMGITFAASILNFVVLTAS 294 L+FY+G L V++S+ PW+ + T +GSPFV F +G AA ILNFVVLTA+ Sbjct: 246 LIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAA 305 Query: 295 LSAINSDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPE 354 LS NS + RML GMAEQG APK +K +RG+P ++L L AV LNY++P+ Sbjct: 306 LSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLNYLVPQ 365 Query: 355 NVFLVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVF 414 + ++ SL V W MI S FR+ + + L FK L F+VF Sbjct: 366 HALELLMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPL-FKALWYPYGNYVCLAFVVF 424 Query: 415 IIALIGYHPDTRISLYVGFAWIVLLLIGWIFKRRRDRQLA 454 I+ ++ P +IS+Y W+ + + + K +R Q A Sbjct: 425 ILGVMLLIPGIQISVYAIPVWVAFMWVCYGIKNKRSAQQA 464 Lambda K H 0.329 0.143 0.449 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: 572 Number of extensions: 29 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: 456 Length of database: 473 Length adjustment: 33 Effective length of query: 423 Effective length of database: 440 Effective search space: 186120 Effective search space used: 186120 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