Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate CCNA_01242 CCNA_01242 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Caulo:CCNA_01242 Length = 531 Score = 437 bits (1123), Expect = e-127 Identities = 243/508 (47%), Positives = 320/508 (62%), Gaps = 37/508 (7%) Query: 16 ADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAG 75 A + AH + LKR L +L+ LG+GAIIGAGIFV+TGQ A+ +AGPAI+LSF+ AG Sbjct: 13 ASIQKEAAHSQ--LKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGPAIMLSFIVAG 70 Query: 76 IACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSG 135 IACALA LCYAE A+ +PVSGSAY+Y+Y TLGE AW +GW LVLEY +TVA GWSG Sbjct: 71 IACALAGLCYAELASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVAASTVAVGWSG 130 Query: 136 YFNKLLALIS------GWIGHDVSLPQT-LAAAPFTVVDGHIQATGMFINLPAVAIIAAI 188 Y L + G D + T L A G + A +NL A IA + Sbjct: 131 YVVSTLHALGINFPMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLNLVAAIGIAMV 190 Query: 189 TGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEG-ASKYGWAG 247 + L VG+++SA VN+ IV IKV V++ FIA +YINP NWHPFIP G ++G G Sbjct: 191 SALLVVGVSESANVNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPEPTGQPGEFGIGG 250 Query: 248 VGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADF 307 + R AAI+FF+Y+GF+AVSTAA EAKNP RD+PIGI+G+LI+CT++Y+ VA ++TG+ F Sbjct: 251 IFRGAAIIFFAYVGFEAVSTAAAEAKNPSRDVPIGILGALIICTLIYMAVAAVMTGVVPF 310 Query: 308 RLLGTPEPVSTALDNYPSLHW---------------LQIIVVIGAVTGLSSVMLVMLMGQ 352 R L +P P++ A+D L W L + IGA+TGLSSVMLV+ GQ Sbjct: 311 RELASPAPIAVAIDRM-GLEWADIPYAAAEGGKLNLLSFAIKIGAITGLSSVMLVLCYGQ 369 Query: 353 PRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLL 412 RIFY+MARDGL+P VF IH KFRTP +GT+++GV+ A I +LG++V++GT + Sbjct: 370 TRIFYTMARDGLLPKVFAEIHPKFRTPWLGTILLGVVIAIAASFLPISLLGDLVSLGTAV 429 Query: 413 AFATVCIGVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSF---LEH------- 462 AF+ VC+ V+ LR P+LPR F+VP G AC+ L Q+F + H Sbjct: 430 AFSIVCLSVIYLRIKHPDLPRPFKVPGGIFTAAAGIAACLFLPYQNFQPMIVHAMNDNPL 489 Query: 463 -WRWMLAWIAIGQAIYFLYGYSHSKLRK 489 + + A+G IY YGY HSKL K Sbjct: 490 PLMILGGYAAVGAIIYIAYGYWHSKLAK 517 Lambda K H 0.328 0.141 0.441 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: 804 Number of extensions: 55 Number of successful extensions: 5 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: 492 Length of database: 531 Length adjustment: 35 Effective length of query: 457 Effective length of database: 496 Effective search space: 226672 Effective search space used: 226672 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 (21.7 bits) S2: 52 (24.6 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