Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_036136362.1 N800_RS06835 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_000768355.1:WP_036136362.1 Length = 491 Score = 281 bits (718), Expect = 6e-80 Identities = 164/417 (39%), Positives = 239/417 (57%), Gaps = 36/417 (8%) Query: 25 ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84 E L R L LV LGVG+ +GAG++V+ G A AGPA+++SF++AA+A AGLCY Sbjct: 30 EVTLKRVLTARHLVMLGVGAIIGAGIFVMTGTAAANYAGPAVILSFVMAAVACGFAGLCY 89 Query: 85 GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELI---- 140 EF + +P +GSAY Y+Y T+GE+ A+ GWNL+L Y+ SSVA WS + + Sbjct: 90 AEFASMMPVSGSAYSYTYSTLGEVVAWFIGWNLVLEYLFAASSVAVGWSGYLNSFLTTHG 149 Query: 141 -GKPIG------EFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMVNKIF 193 G P +S + + + G + P AV+I+ ++GL G+ +SA VN + Sbjct: 150 AGVPAALAQAPFHYSAETSSFVSTGSIVNLP---AVLIVAAISGLCYRGITQSAWVNALI 206 Query: 194 TCINVLVLCFIVVSGFVKGSIK--NWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSG 251 I V V+ + GF I NWQ + EGG FG GV+ G Sbjct: 207 VAIKVTVI--VAFLGFAAQYINPDNWQ------------PFIPENEGG-TRFGTEGVVRG 251 Query: 252 AATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLD 311 AA F+A++GFD ++T E KNPQ+ +P+GI+ SL +C + Y V+A LT ++PY LD Sbjct: 252 AAVVFFAYIGFDAVSTAAGEAKNPQRDMPIGILGSLAVCTVLYIAVAATLTGLLPYPQLD 311 Query: 312 IDSPLP---GAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368 P+ A+ GW K AV IG++ LS+ +L + PR+ YAMA+DGL+ K Sbjct: 312 TAKPVATALEAYPTLGW--LKMAVEIGAIAGLSSVILVMLMGQPRIFYAMAKDGLMPKIF 369 Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY 425 +++ + +TP + TV G +AA+MA L L L DL+S+GTLLA++ V A VL+LRY Sbjct: 370 GRVHPKFQTPYVGTVIVGVVAAIMAGLLPLDFLGDLVSMGTLLAFATVCAGVLILRY 426 Score = 47.0 bits (110), Expect = 2e-09 Identities = 39/135 (28%), Positives = 61/135 (45%), Gaps = 12/135 (8%) Query: 471 KSILSPK---NVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTG 527 K L PK V P + + + G++AA++ + + LG + ++ GTL A + Sbjct: 361 KDGLMPKIFGRVHPKFQTPYVGTVIVGVVAAIMAGLLPLDFLG-DLVSMGTLLAFATVCA 419 Query: 528 SVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWML 587 VL I R + F+VP V+ L + +YL Q + W W + Sbjct: 420 GVL--------ILRYTRPDLQRPFRVPGAIVVCSLGVLSCLYLFWQPFKDHWQVMLGWTV 471 Query: 588 IGFTIYFGYGIWHSE 602 IGF IYFGYG +S+ Sbjct: 472 IGFVIYFGYGYRNSK 486 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: 783 Number of extensions: 40 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