Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_057508922.1 ABB28_RS12355 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_001431535.1:WP_057508922.1 Length = 491 Score = 278 bits (712), Expect = 3e-79 Identities = 168/429 (39%), Positives = 235/429 (54%), Gaps = 46/429 (10%) Query: 25 ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84 E+ L R L L+ LG+G+ +GAG++V+ G A +AGPA+ +SF++A LA LAGLCY Sbjct: 30 EATLKRTLTAKHLILLGIGAVIGAGIFVMTGQAAAFHAGPAVTLSFVLAGLACALAGLCY 89 Query: 85 GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATF-------- 136 EF A +P +GSAY YSY T+GE A+ GW L+L Y+ ++SVA AWSA Sbjct: 90 AEFAAMMPVSGSAYSYSYATLGEGMAWFIGWCLVLEYLFASASVAVAWSAYLLSFVTTTL 149 Query: 137 -----DELIGKPI----GEFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESA 187 D L PI G+F N P AV+I+ +TGLL +G+ +S Sbjct: 150 HLPFPDALSSAPIAWEGGQFIASGQLFNLP----------AVLIVAAVTGLLYVGISQST 199 Query: 188 MVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSG 247 VN I I V V+C + G NWQ + G F FG+SG Sbjct: 200 FVNGIIVAIKVSVICLFIGFGASHIDTANWQ------------PFIPENTGTFGEFGWSG 247 Query: 248 VLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPY 307 VL + F+AF+GFD ++T E K+PQ+ +P+G++ SL IC I Y V LT ++PY Sbjct: 248 VLRAGSIVFFAFIGFDAVSTAAGETKDPQRNMPIGLLGSLAICTIIYVIVCLVLTGLLPY 307 Query: 308 FCLDIDSPLP---GAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLL 364 L P+ A+ W K AV IG++ LS+ +L M R+ Y ++ DGLL Sbjct: 308 QQLGTAKPVATALEAYPQLAW--LKTAVEIGAIAGLSSVVLVMMMGQTRIAYTISRDGLL 365 Query: 365 FKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424 +FL K++ R KTP +AT+ G IAA +A + L L +L+S+GTLLA++ V VLVLR Sbjct: 366 PRFLGKVHARFKTPYVATIIVGVIAAALAGMMPLNVLGELVSMGTLLAFATVCIGVLVLR 425 Query: 425 YQPEQPNLV 433 Y +P LV Sbjct: 426 Y--TRPELV 432 Score = 42.4 bits (98), Expect = 5e-08 Identities = 33/117 (28%), Positives = 56/117 (47%), Gaps = 9/117 (7%) Query: 488 IVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKT 547 + I G++AA + + + VLG E ++ GTL A +C+ V + + +PE Sbjct: 381 VATIIVGVIAAALAGMMPLNVLG-ELVSMGTLLAF------ATVCIGVLVLRYTRPELVR 433 Query: 548 KLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604 F+VP ++ L + L + W F W ++G IYFGYG+ +S+ A Sbjct: 434 P--FRVPMAWLICPLGALACLTLFAMAFREHWHLFVGWTVLGLLIYFGYGMRNSKLA 488 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: 823 Number of extensions: 56 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: 491 Length adjustment: 36 Effective length of query: 586 Effective length of database: 455 Effective search space: 266630 Effective search space used: 266630 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 24 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