Align high affinity cationic amino acid transporter 1 (characterized)
to candidate CCNA_01242 CCNA_01242 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Caulo:CCNA_01242 Length = 531 Score = 254 bits (649), Expect = 7e-72 Identities = 160/456 (35%), Positives = 249/456 (54%), Gaps = 53/456 (11%) Query: 14 LRRKVVDCSRE--ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFL 71 L++ + +E S+L R L +L++LGVG+ +GAG++VL G VA NAGPAI++SF+ Sbjct: 8 LKKSIASIQKEAAHSQLKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGPAIMLSFI 67 Query: 72 IAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARA 131 +A +A LAGLCY E + +P +GSAY Y+Y T+GE++A+I GW L+L Y + S+VA Sbjct: 68 VAGIACALAGLCYAELASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVAASTVAVG 127 Query: 132 WS----ATFDEL-IGKPIGEFSRQH---------MALNAPG-----VLAQTPDIFAVIII 172 WS +T L I P+ + + A+ APG + T ++ A I I Sbjct: 128 WSGYVVSTLHALGINFPMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLNLVAAIGI 187 Query: 173 IILTGLLTLGVKESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQ--LTEKNFSCNNND 230 +++ LL +GV ESA VN I V+VL + G + NW + E Sbjct: 188 AMVSALLVVGVSESANVNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPEPT------- 240 Query: 231 TNVKYGEGGFMPFGFSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLIC 290 G+ G FG G+ GAA F+A+VGF+ ++T E KNP + +P+GI+ +L+IC Sbjct: 241 -----GQPG--EFGIGGIFRGAAIIFFAYVGFEAVSTAAAEAKNPSRDVPIGILGALIIC 293 Query: 291 FIAYFGVSAALTLMMPYFCLDIDSPLPGAFKHQG--WEEAKYAVA-------------IG 335 + Y V+A +T ++P+ L +P+ A G W + YA A IG Sbjct: 294 TLIYMAVAAVMTGVVPFRELASPAPIAVAIDRMGLEWADIPYAAAEGGKLNLLSFAIKIG 353 Query: 336 SLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFL 395 ++ LS+ +L + R+ Y MA DGLL K A+I+ + +TP + T+ G + A+ A Sbjct: 354 AITGLSSVMLVLCYGQTRIFYTMARDGLLPKVFAEIHPKFRTPWLGTILLGVVIAIAASF 413 Query: 396 FELKDLVDLMSIGTLLAYSLVAACVLVLRYQ-PEQP 430 + L DL+S+GT +A+S+V V+ LR + P+ P Sbjct: 414 LPISLLGDLVSLGTAVAFSIVCLSVIYLRIKHPDLP 449 Lambda K H 0.324 0.138 0.417 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: 790 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 531 Length adjustment: 36 Effective length of query: 586 Effective length of database: 495 Effective search space: 290070 Effective search space used: 290070 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 (21.6 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